Pretty easy question, there are plenty of characters that ignore hindering terrain via Avengers Intiative, Superman ally team ability, traits etc.

The Batman cowl allows you to use stealth when next to blocking terrain if you already have the batman ally team ability.

So can Superman still see my cowled batman if he's next to blocking terrain rather than on hindering?

Quote: This character possesses "Batman Ally Team Ability Symbol". If the character already possesses "Batman Ally Team Ability Symbol" and is adjacent to a wall or square of higher elevated terrain, lines of fire drawn to it are blocked when it is not your turn.

Blocked, not stealthed, so no Superman could not see him. This has nothing to do with hindering.

^ Correct. Superman Ally and similar abilities ignore hindering for every purpose (no stealth, no messing with movement, no defense bonus when shooting through it, etc) but do not ignore abilities that may be related to hindering. Cowl creates a new game rule that has nothing to do with hindering so Superman Ally has no affect on it.

Sorry confused the cowl with the very similar but different Tabapp trait on Batman that reads:

HIDING IN THE SHADOWS: When Batman is adjacent to a wall, blocking terrain, or a square of higher elevated terrain, the square he occupies is considered hindering terrain for line of fire purposes.

I assume Supermam can see through this since it considers the square hindering terrain?

Yes, since someone using the Superman TA ignores hindering terrain, he would ignore the hindering terrain "created" by that special power.