If an attacker has a smartgun system and is attacking from cover does he get the -1 for attacking from cover? For +1 total assuming those are the only 2 modifiers. Or is the attacking from cover modifier negated making it +2?

Your +1 reading is correct. Shooter gets a +2, but shooting from cover partially abrogates that bonus.

but should the now in smartlink included gun-cam not take care of that?

IANAGE (I am not a gun expert) but it seems to me that firing a gun is a matter of hand-eye coordination. When the "eye" you are trying to coordinate together with your hand is not where your body is accustomed, I can only imagine that it would be more difficult. In other words, even if the smartlink helps, it's still harder (+1 total instead of +2) than firing from a non-covered position using your normally-positioned eyesight.

DS

This has been gone over on multiple threads. The -1 from firing from cover should generally still apply because it's not a sighting issue but a body positioning issue. Yes, the smartlink negates the penalty. But in turn, the smartlink doesn't provide as much of a bonus due to being unable to bring the gun to bear as accurately as you would if you were not partially hiding behind something.

If you choose to change this rule, feel free. But that opens up the can of worms of negating all kinds of other penalties because smartlinks should help with those problems, too. Smartlinks are already helping by giving a blanket +2 dice.

Yeah, I was planning on ruling that it doesn't negate cover (so +1 in the OP case) but I just wanted to make sure that there wasn't some obscure passage in the BBB or Arsenal that said differently.