Our startup uses affiliate channel for user acquisition, and we are ripping off all of our partners by the tune of 30-40%. As an employee am I doing anything illegal by participating?

While I can't speak to the exact legal ramifications, this is an incredibly short-sighted business move.

If affiliates work as a channel for you, it will work for your competitors. Any decent affiliate can do the math and get a sense for when they are getting "shaved" and will happily move to a competitor.
Good affiliates are very, very good at SEO. Defrauded affiliates can seriously destroy your search rankings and your reviews.

Here is a final example. You are an early start-up and Adwords is performing well for you. Would you intentionally + egregiously violate all of their ToS and get your ad account banned forever?