RAW, these improvised weapons probably do not deal the normal 1d4+DEX damage.
Each of these objects specify that the user should treat them as an improvised weapon while making their special attack, which would imply 1d4+DEX damage on a hit. However, they also specify what should happen if the attack roll is a hit, such as the acid vial dealing 2d6 acid damage as you mentioned. This specific effect replaces the general effect of landing the hit.
While it would certainly make sense that being beaned by a glass bottle would deal damage, all of these hit descriptions are missing the important word extra when they are describing their on hit effects. All of the effects that I could find which have an attack deal damage on top of its usual damage, such as the Rogue's Sneak Attack feature, the 5th level enhancement of the greenflame blade cantrip, and magic weapons such as the Frost Brand list the damage as extra damage. If the vials were intended to also deal their improvised damage, they would have their effects listed as extra.