Thanks to Ploni for starting this off. Shu"t Halachos Ketanos 1:137 (quoted in Pachad Yitzchak (Lampronti) Erech Tashmish, as well as the Kaf Hachaim above) gives two possible reasons for not saying it:
אם בדרך הטבע אין חוש המישוש חרפה לבע"ח אלא שהנהיגוהו במקומות האסורים וכיון שרוב ביאות שבעולם הם באיסור ובאפקירותא אפשר שלא רצו לתקן ברכה על זה. א"נ משום שהוא מזיק לגוף כמ"ש הרמב"ם ז"ל (בפ"ד מדיעות) ואין מברכין על הקלקלה ואפשר שאם יהיה בשעת רצון ושצריך לדבר ויטהר עצמו וינקה היטב במקום קדוש שיברך ועתב"ט:
- Most relations that take place are prohibited, and therefore Chazal did not want us to make a Beracha on them
- It is harmful to the body.
Therefore, the Halachos Ketanos concludes that it is possible that if one feels like he needs to be Motzi Zera, and the relations are done properly, at the right time, and he is clean and in a proper place, he should make an Asher Yatzar. He also later suggests the opinion quoted above, that one should use the bathroom and have both emptyings in mind. This is also suggested in this Chabad article.
(Although I'm not really sure that I understand either answer, I would propose that Chazal did not institute an Asher Yatzar on this because it will often be a while until someone is clean and in a proper place to make such a Beracha.)
Rabbi Gamliel Rabinowitz here (p. 59) brings a few other suggestions in addition to a very long summary of the above and other sources.
- If it would be blocked up, you would still be able to survive.
- Originally since Tevilas Ezra was required, one could not make the Beracha until after Tevilah, and it never became required by Chazal since then.