The number in brackets still refers to the skill level (1 to 5), but the skill is separate from the ones in your skill list. For the most part, I think corresponding skills have the same or similar effect, chance to hit, etc. One exception is that Frost on a weapon ignores the target's resistance, so is much more powerful than Freeze.
Assassin's Kiss(1) would give you an extra chance for double damage to be applied. AFAIK (not using the skill), the "Works with Assassin's Kiss" description applies to any short sword, dagger, knife, etc. that is shorter than a certain length, and does not specify a skill level.