The sin of Onan has been specifically addressed in Sacred Tradition. Pope Pius XI writes in
Casti Connubii (Nos. 54-55):
Since, therefore, the conjugal act is destined primarily by nature for the begetting of children, those who in exercising it deliberately frustrate its natural power and purpose sin against nature and commit a deed which is shameful and intrinsically vicious.
Small wonder, therefore, if Holy Writ bears witness that the Divine Majesty regards with greatest detestation this horrible crime and at times has punished it with death. As St. Augustine notes, "Intercourse even with one's legitimate wife is unlawful and wicked where the conception of the offspring is prevented. Onan, the son of Juda, did this and the Lord killed him for it."
Pope Pius XII specifically recalls Casti Connubii in his 1951 Allocution to midwives, stating:
that every attempt of either husband or wife in the performance of the conjugal act or in the development of its natural consequences which aims at depriving it of its inherent force and hinders the procreation of new life is immoral; and that no 'indication' or need can convert an act which is intrinsically immoral into a moral and lawful one.
This precept is in full force today, as it was in the past, and so it will be in the future also, and always, because it is not a simple human whim, but the expression of a natural and divine law.
Pius XII continues, addressing the scientific basis for natural family planning (remember that Roetzer was researching an effective systematic means of NFP as early as the 1930s):
It is necessary first of all to consider two hypotheses. If the application of that theory implies that husband and wife may use their matrimonial right even during the days of natural sterility no objection can be made. In this case they do not hinder or jeopardize in any way the consummation of the natural act and its ulterior natural consequences. It is exactly in this that the application of the theory, of which We are speaking, differs essentially from the abuse already mentioned, which consists in the perversion of the act itself. If, instead, husband and wife go further, that is, limiting the conjugal act exclusively to those periods, then their conduct must be examined more closely.
It is in this sense that Pope Paul VI elaborates more fully in Humanae Vitae, namely that the natural fertility cycles are created by God. When married couples learn of these cycles and seek to make use of them in submission to the will of God, they make use of God's own creation in that singular act which is the most intimate expression of human love possible (more intense and more intimate love is possible, but in such cases, one of the parties is God Himself).
Moreover it is absolutely clear that NFP can be used for selfish reasons, in which case it really is no different from contraception except in one respect: practicing NFP to avoid pregnancy requires abstinence. Moreover, it is not a decision that is easily made in a single moment for many months (or years) at a time, as is clearly the case with sterilization, for example. Couples must address their fertility each month, even in the worst case, and so even though the worst case (selfish use of NFP) is still the stuff of sin, the discipline in and of itself contains the means of returning to God, if only the couple will let God operate once again.
Your illustration of using perforated condoms as a contraceptive that is in line with the Natural Law (and therefore with the precepts of the Church) begs for a better explanation. There is a fundamental difference between a specific exception addressed by Papal and Magisterial teaching (e.g. NFP) and another specific exception not addressed by any Papal or Magisterial teaching (e.g. perforated condoms as a contraceptive). Absent the specific exception, the general rule (i.e. no contraceptives) must apply.
Keep in mind, moreover, that the intention of the couples using perforated condoms to collect a sperm sample for diagnosis of male infertility is fundamentally different from the intention of the couple who expects to use them to avoid pregnancy. Especially if used during the fertile period, the use of perforated condoms would constitute a specific intention of going against our created fertile nature, coupled with a material act (the use of the perforated condom) that might otherwise be allowable. With NFP, this is never true: the couple's material act is always completely open (and this completeness matters). The intention is expressed in the timing of conjugal relations, and the knowledge is readily available so that the couple refrains from the material act at the time when pregnancy could occur (i.e. the fertile time). One is forced to wonder how this alignment of intention and action could be accomplished by the use of perforated condoms, especially if NFP is not practiced (which precludes systematic knowledge of the fertile time and the non-fertile time) or if perforated condoms were only used during a known fertile time (in which case it is difficult to align the couple's action with their natural fertile state at the time).
This differs fundamentally from the practice of NFP. The underlying intention of NFP is to observe and apply knowledge of our created bodily nature as a means to determine when we as couples are fertile and when we as couples are not fertile. The cyclical fertility is created by God; the perforated condom is not. Moreover, we are not talking about hairstyle or fingernail polish here: we are talking about the most intimate natural expression of human love in complete gift of self from husband to wife and from wife to husband. Thus, prudential principles that might apply in lesser areas must be submitted to providential principles here.
Besides all this, you would have to be phenomenally misguided to expect a perforated condom to function as a viable contraceptive, particularly if used during the fertile period. Perfectly produced contraceptive condoms are at best only 97% effective when used properly by the couple. And this poor effectiveness is for couples who use them all the time, including during the 75% of the time when a couple's natural infertility prevents conception altogether. Moreover, there is ample evidence of greatly reduced rates of effectiveness in the poorly produced and poorly distributed condoms that have been sold as fool's gold in the effort to prevent AIDS in Africa: perfect-use effectiveness rates of these condoms fall to 80% or less (and this also helps to explain why condoms have actually contributed to the spread of AIDS in Africa: that kind of "protection" is worse than none at all because it provides a false shield that also increases rates of promiscuity, which is what causes the spread of AIDS in the first place). If you were using a condom as a contraceptive and it had a hole in it, then your best comparison of effectiveness would be to condoms that have defects in manufacture or are damaged in distribution (as many of the condoms distributed in Africa are).