Firstly, the rulebook says that to move through other ships, you just kind of hold the template above and guesstimate where you'll end up. Compared to how exact most everything else is, is there some other way this is handled? Especially in tournaments and such.

Second, I have a misprint Ion Cannon. It has both the symbol for cannon and missile printed in the lower left icon space. I'd obviously be using it as a cannon, but is a misprint even legal to use at a tournament?

You can use maneuver templates or other markers to mark the position of a ship you need to move through on the table.

Misprints are fine, as long as they are used as intended.

Actually Litko make some very cool little marker templates that just fit into the front or rear nubs so you can remove a ship that's in the way and then replace it later in its exact position. Really handy.