Yes in ED:AoL you always roll only one FU dice (it differs from FU core in this)
jase:
Can you have both bonus and penalty dice?
No bonus and penalty cancels each other out, you either rolls bonus or penalty (or neither if you have the same number of bonuses and penalties)
jase:
Is there a limit (realistic or set) for the number of penalty dice?
I don't think you have a maximum number of dices but I have to say normally you would get 1-3 and I have never seen anything beyond 5... To be frank anything beyond 10 sounds absolutely pointless (probably even less)