BoxOfSnoo: OK here's what seems to be the definitive answer.
First of all, presume the difficulty levels start at 0,
0=Trainee, 1=Rookie, 2=Hotshot, 3=Ace, 4=Insane
1) No cheats (of course)
2) Difficulty level "Ace" or greater
3) level points * (difficulty level - 1) / 2
4) subtract the modulus of the above into 100 (So, something like 34567 would get you 34500)
This is from the source code, available on the web. I didn't do extensive searching through the code, so they may have slipped something in there that resets them to zero but I seriously doubt it.
You can get skill points on hotshot.
I've been getting them consistently; I'm pretty sure I've found all secrets and killed all enemies, a well as rescuing all hostages.