I'm a GM for my group that plays BC (3 humans, 1 space marine) and I wanted to eventually give them their own spaceship because I thought it'd be really awesome to have a ship going to various planets and destroying some imperial navy ships along the way.

Now we're playing using the guidelines, creatures, and items of the 40k universe, but most of the planets/other places they've been have been random (Like a desert planet called Ellon with one lake and the majority of life on the planet is around the lake).

...Anyways I was wondering if anybody had done something like this before and if they had armor, health, and damage values for ships; I've got a pretty good idea on what they should be, but I just wanted to know if it had already been done because I haven't seen anything around for it.

You may want to have a look in Rogue Trader, which specifically covers space ships and such. Ships get Void Shields, armour and Integrity.

Void shields reduce the number of incoming shots by that amount, armour reduces the damage the ship takes (like player armour) and anything left takes away ship Integrity (think of these as wounds.)

A bog standard Imperial vessel is on P211 of said book.

It's a small one but it gives the ship

1 Void Shield

18 Armour

33 Wounds

This might not seem a lot but then this is all relative compared to other anti-starship weapons. Anti infantry would likely do bugger all!

Anti infantry would absolutely do bugger all. The only way for marines (space or otherwise) to really damage such a vessel is through the judicious application of demolitions. Also 'wounds' above should read 'hull integrity,' I think. Too lazy to pull out a book right now.

The stats make more sense when you realize that most damage is X(d10+[2-4]) where X is half the number of degrees of success you got up to a cap, said cap varying from weapon system to weapon system, or 1d10+2 ignoring armour. 3d10+9 isn't tremendous damage, but it's enough to crack that armour value of 18 and do a little bit of hull damage besides.

This might not seem a lot but then this is all relative compared to other anti-starship weapons. Anti infantry would likely do bugger all!

...and by Anti-infantry weapon, we mean las cannons and krak missiles.

IIRC, Turrets (for killing small crafts and torpedoes) include such things as lascannons (and presumably long barreled autocannons). And they explicitly cannot harm ship-scale targets.