Custom skins will not get you VAC bans
VAC ONLY bans bad memory hashes.
VAC 2.0 matches all your memory hashes [each time you join a VAC secure server] to a list of "bad" hashes.
if you are matched positive to them, you get banned.
Banns can take anywhere from 1 second to several years to take in effect.
I had a friend who hacked on 1.3 He was banned August of 09.

If your account is hacked, and they hack, yeah, it still effects you.
Sorry mate.

Im not 100% sure of how Cracked servers are done via Valve. However, Cracked servers give off bad Memory hashes.