Also whats that all on its own?
I guess it unsets them (nether really tried that method) but yeah unset %var should work.
'%var =' (followed by a space or end of line) gets mapped directly onto 'set %var' early on by mIRC's interpreter. thus '%var = value' as a command is exactly equivalent to 'set %var value' - remember that /set modifies local variables and only creates a global variable if a local one of that name doesn't exist.
the procedure that does this mapping is a bit greedy: it also plays a role in the evaluation of the arguments to an identifier (which is a slightly different evaluation routine in a number of ways). this really is silly, but at least it allows me to produce proof of the above claim :P
//echo -a $+(a, %var =, b) and $replace(a, a, %var =)