Rifle/Pistol Stat Bonuses
It has been complained about hundreds of times in these forums, right along side with the auto attack having to be toggled manually. While I have seen the auto-attack issue mentioned as a bug to be addressed, I have yet to see anything from ANet regarding the stats issue. I would love to see it addressed though, that is a large hit to your potential damage and/or survivability.
So in short: ‘yes’ :-)
Switching to a kit makes you lose weapon stat bonuses. If you like using kits (you happen to play an engineer don’t you), you’re weapons’ stats are rather useless.