Sorry, no, I don't acknowledge this as more common.
I thought you meant scripts like that, query blocker scripts.
The only ones that would be are those that arbitrarily block nicknames based on modal user input (an invalid case, as I mentioned), or flood control scripts. For flood control, there are alternatives out there (like mIRC's builtin flood control), and worst case scenario is that you accidentally trip your flood control with /query, so it's not a huge incompatibility.
Also, given how *common* query blockers are, how easy they are to script, and how many alternatives are available (server-side ignore, /ignore, mIRC flood control, etc.), breaking a few of these scripts becomes less of a big deal. At least in this case, users have alternatives, and the simplicity of these scripts (they all seem to be < 100 lines of code) means it is trivial to fix them.
This are compatibility issues, not everyone knows how to fix them.
'server-side ignore', what if the network doesn't support it?
'mIRC flood control', you can't customize it (change my nickname, etc.)
'/ignore', before flood occurs?