It can be damaged, but only limited. Bullets don't harm it at all (except shooting the glass, which does some very minor damage I believe). Rockets do quite some damage, but by default its health will require several rockets to kill it off.

You can tweak around the health of the APC by setting a cvar on the server, I think it's zapc_health or zapc_max_health, I can't completely remember anymore.

Every time you take damage, the HUD in the APC should flash red, so getting inside it and have somebody damage you is the quickest way to find out if it works.

I suppose it's possible that other addons are messing this up, but I haven't come across one yet.