The shoujo-ai/yuri debate is much worse because there are fiercely held and mutually exclusive opinions on what the tags mean in the first place (and Mangadex is pretty lax about laying down clear and complete definitions for all the tags, so finding the official stances on this stuff is hard).
Whereas yaoi/shounen-ai is pretty clear cut: Is there a sex scene, or not?
Someone once tried to enlist my help in sorting through all the series that are tagged as both (since I've somehow become one of the more visible commenters in BL-space, and have contributor privileges). I essentially said "no," partially because there's a lot of Yaoi I never want to lay eyes on, but also because of complicating and ameliorating circumstances:
- It's not clear what to do about anthologies (and having more than one completely unrelated story in a particular BL volume is REALLY common)
- Whenever series are tagged with both, in practice it just means it's yaoi. The risk of ambiguity is actually quite minimal.
Anyway, in response to your actual questions:
1. Some of the tags give a definition if you click on them (in addition to search results).
...Unfortunately the definitions were copy-pasted from somewhere early in the site's development and do not always reflect current use (For the most blatant definition drift see "smut" https://mangadex.cc/genre/32 which has since been (officially, I beleive) co-opted to mean "contains sexual content", since mangadex didn't want old Batoto's mature content flag for whatever reason) nor do they even exist for many of the more recent tags.
2. I'm not sure what official policy is, but aside from the uncertain consideration of anthologies as I just mentioned, they are mutually exclusive by tradition, more or less. (Though it's possibly not 100% consensus on that point, I think; a handful of people may have used both side-by-side to indicate a series that has some sex but also a large proportion of more general-audience romance themes, or something along those lines.)
