They mean different things. Every vote counts: every vote is important; every vote matters. The vote is counted: the ballot papers are counted and the candidate with the most votes is elected.

In other words: 'Every vote matters' or 'Every vote is important'

"Every vote is counted" can mean: 1) The election is fair, the election officials are honest, and every vote gets counted, OR 2) The election is over now, all of the votes have been counted and the totals are complete. "Every vote counts" means: Every vote matters. Be sure to get out and vote. Don't stay home because you think you know who will win. Go to the polls. Every vote counts.