So with Coelcanth's effect, if you were to summon a Deepsea Macrotrema, and then use his second effect to destroy Macrotrema, would Macro's effect still kick in? Or would it be negated?

Deepsea Macrotama is the one that gives WATER monsters a boost when it's sent to the Graveyard, correct? If so, then yes, Macrotama will still get its effect.

http://metagame.com/yugioh.aspx?tabid=33&ArticleId=9301

It's somewhere in that article.