Quadruple downvotes for saying "Benchmark it" to this question. The real answer is that every use() past the first is only a hash lookup. There's no abuse of the compiler and you should feel very safe in using the same thing from many places.
Caveats are of course, that $class->VERSION eq '...' or die "..." and $class->import(...) are also possibly implicated but neither of those are compiler tasks and you ought to already know if you care about the overhead of each and whether you're invoking them. I can't imagine someone using CGI::Application is going to care about the additional cost of one cheap method call.