1. Is negative and unholy damage the exact same mechanically?

Yes, I believe, depending on what you mean by "unholy". An unholy weapon (as in, unholy blessed) doesn't necessarily do negative damage.

There's actually a helpfile with this stuff in. Not sure what you have to search for, but try "damage". It lists what kind of damage messages relate to which kind of attacks.

2. If so, are there any situations where they wouldn't be?

Don't think so.

3. Do casted spells by necromancers or ap's count generally as unholy, if not generally, any of them specifically?

If it does, it would only be the ones that do negative damage. Note that ap's have an edge that makes their fireballs do negative damage, if I'm recalling correctly. But an ap's iceball is not unholy, damage-wise, for example.

Vamp touch is, I believe, negative damage, so it might help against that.

4. If so, does Forsaken Thoughts technically help against them to a degree then?

Left for Nep or someone who has taken it.

5. Forsaken obviously isn't resist holy/unholy. Would you be generous enough to give us numbers on the redux? Is it greater than 15%?

Left for Nep or someone who has taken it.