There is no backwards compatibility issue with added behaviour.
Using an alias doesn't account for all the ways "you" open a window. Namely, a script can still use /!query to bypass the alias, secondly, there are many non-command ways to get a query window: selecting "query" from the Notify window is one of them-- that behaviour is not overridable, nor is it tied to /query.
For what it's worth, the behaviour has to do with a somewhat archaic convention mIRC used to use regarding event triggering. In the past, the convention was that no event would ever fire if there was a command equivalent to trigger it. Recently, however, ON CLOSE was changed, and therefore it's probably time that ON OPEN changes as well for consistency's sake.