Can you use Horton Salms re-roll ability with proton torpedoes, or do secondary weapons not benefit from abilities?

You can use his ability with any secondary weapon as long as you meet the range requirements of his ability.

Abilities work like they say they work - if an ability modifies your attack roll, it works on any attack roll. (Marksmanship,e.g.)

If an ability applies to a primary weapon, then it can't be used with secondary weapons (Howlrunner, if I remember correctly).