Can you use pilot card abilities with secondary weapons (i/e Boba's "When attacking or defending, you may reroll 1 of your dice for each enemy at Range 1" with a "Mangler" Cannon?

Yes. Unless the ability mentions the weapon type. So if it says 'when performing an attack with the primary weapon' then it only works with that.

Is there anything that say "Primary" or "Secondary" weapon?

No?

Then you have your answer to how restricted Boba's ability is to use.