Why are links removed after transliterating usexes?
That's not the point. This is a merely technical issue that links are stripped from the text before entering the transliteration module and then (seemingly only in usexes) the output of the transliteration module is stripped from links again. The second part is what shouldn't be happening.
Thanks. And you should also consider my side note if you ever have time (i.e. remove_links("foo[[Category:Bar]]baz") should really return "foobaz" and not "fooCategory:Barbaz").
Well that's only one case. It also needs to make sure that "[[:Category:Bar]]" becomes "Category:Bar" and also handle interwikis the same way. And the regular expressions would need to account for cases like "[[category:Bar]]" and "[[ Category : Bar]]" or worse. I hope it doesn't sound like I'm demanding things. These are just suggestions for when you have time, since it might take some work to figure out all the cases.