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We haven't been using commands from the youtrack plugin, so perhaps we just got lucky in this regard.
I'm looking to see if there's a way to customize the parser, but it looks like the `#` is just always used to mark the start of the pattern. This is coming from https://github.com/mstrap/bugtraq (which is the system employed by gitblit) just in case it's interesting...
update: lol, having read the bugtraq docs a bit more carefully, there is a whole regex pipeline I can take advantage of, so I can totally switch the pattern from ids starting with `#` to use some other character, or enclose in `[]` or whatever. Totally possible, but until we have the need to run custom commands, I suspect we'll stick with the default.