If a character wants to use different weapons with his Dual Shot (for example Bolt Pistol and Compact Las Pistol) - how should I determine bonuses/penalties for BS? For example - those weapons have different Range and character can even have no proficiency in one of the weapons.

Will bonuses and penalties be counted as 'average'?

If my understanding of the RAW is correct, all bonuses and penalties on a single attack stack. Since Dual Shot is treated as a single attack, then I would probably rule that this is the case here as well. But I would have to look at the errata again, to make sure that it's not already covered there. Hope that helps.

The easiest way to resolve it is

Make the attack: if the check would make a single shot with either weapon hit, it's a Dual Shot ... if only one, it's a Single Shot ... if neither, well ...

Keep in mind that per the rules the benefit of one red dot laser sight transfers to both weapons. Which should probably apply to all bonuses/penalties but those specific to the weapon (like range and proficiency).

Interesting....

Strange that this has never come up in our own game yet.

If I was to give an on the spot ruling, I'd say that if you are Dual Shot-ing with weapons that have different ranges, you suffer the penalty for the weapon that suffers the larger penalty (has the shorter range).

Of course, my players would argue the point....