Using wall plates will always give a much more refined, professional appearance to your setup. Running the wires straight through the wall might be preferred in some situations (i.e., wall-mounted surround speaker, where the hole is hidden behind the speaker) and even then, I would still use a basic wall plate with a hole cut out, and maybe even snake skin from the wall to speaker. But a bunch of speaker cables running out of the wall behind or near your equipment rack makes for a sloppy, amateurish look, not to mention, if you decide to move your rack at some point, you're most likely SOL, and will end up having to cut and splice, rather than just cutting a new length and plugging into the wall plate from the new location.
Just my $0.02.