There are six skills checks - Speed, Sneak, Fight, Will, Lore and Luck, that I can use Clue tokens for more dices.

Can I use clue tokens with special skills like spell, combat and horror checks to add more dices?

Yes: Combat/Horror/Evade/Spell checks are specialized types of Fight/Will/Sneak/Lore checks, so anything that grants a bonus to the generic stat also grants a bonus to the specialized check. The reverse is not true though: you can't use a handgun to help you pass a Fight check to pry open a grate in a wall.

Tibs explained it well. I usually think of it in this way: a Fight check is any check in the game that uses Fight. If you get a bonus to Fight, it applies to all types of Fight checks: Combat checks, checks to close gates based on Fight, checks in encounters that use Fight, and so on. A shotgun will only provide a bonus to combat checks, and not any of the other types (it does not help you close gates).

All cognac is brandy, but not all brandy is cognac...