Base Vipers appear normally, but are phased out by the new higher tier Vipers in the same way ADVENT units go from basic -> advanced -> elite. The special Vipers (Naja and Sidewinder) appear in addition to the plain ones and also have later game upgrades.

How much different in stats is a Naja and Sidewinder compared to a base Viper in the same tier?
And what makes them different other than Naja is a sniper?

Naja's have lower health and dodge scores than regular vipers, in addition to higher aim and their sniper abilities. Sidewinders have good mobility, and a bonus to aim when they are flanking a unit. 'Sidewinder' was also the name used in Long War for Thinmen who had the Lightning Reflexes perk, so it's possible X2 Sidewinders do as well but I'm not sure.

Originally posted by FowlJ:

Naja's have lower health and dodge scores than regular vipers, in addition to higher aim and their sniper abilities. Sidewinders have good mobility, and a bonus to aim when they are flanking a unit. 'Sidewinder' was also the name used in Long War for Thinmen who had the Lightning Reflexes perk, so it's possible X2 Sidewinders do as well but I'm not sure.

someone on this forum about the mod said that Naja have squadsight. This makes them pretty nasty when you run into them and don't take them out.

Also sidewinders have an ability called "hit and run" where if they shoot and hit someone they get another action to move. Naja always worry me, but many of the other aliens can be a lot nastier.