Some examples in article space (so not with a namespace prefix), where the parenthesized part is really a part of the subject's name:
I.m.o. there shouldn't be anything stripped (by default) in these links' labels. Of course, as with page titles containing a comma, if the parenthesized term (or the comma, plus what follows) is really a part of the article subject's name, and the editor doesn't want it to get stripped off, then s/he just shouldn't enter a pipe. I couldn't find any picnic/pebcak tag to add to this ticket, so if in (almost) all cases of page titles that end with the parenthesized term is part of the subject's name —also on other (e.g. non-alphabetic script?) projects— I guess this could better be excluded from the pipe trick.