Some people experience abdominal discomfort from the ejaculate in anal sex. Semen can make its way into the bowels and cause cramping that feels like a stomach ache. This isn't an issue in vaginal sex. But I think the reason semes ask in yaoi is that it's a kink, makes it seem kinkier if they ask. And you're not an idiot.
It's a nuisance to clean up after..I mean if both partners like to snuggle after -sex and won't immediately clean up after the deed,the cum will stay inside the arse and might give the bottom a slimey feeling...and it might take several bowel dumps before all the nasties are out.It may also lead to bacterial infection if rectum has wounds or tears. ^^
It upsets the bowel movements often leading to diarrhea .. ^^"
Call me idiot but I really don't know. Aside from being scared of getting AIDS, is there any other reason why the Seme can't come inside the Uke? Because in Some manga, even if Seme-kun didn't had any partner before Uke-chan, he's still not allowed to c*m inside. (=^-ω-^=)