I guess it depends on how fussy you want to get on the term "weapon".
Acid flasks are considered
splash weapons, which are specifically designated as a ranged weapon, but also one that doesn't require proficiency (I don't think that last part really matters for this purpose, though).
A splash weapon is a ranged weapon that breaks on impact, splashing or scattering its contents over its target and nearby creatures or objects. To attack with a splash weapon, make a ranged touch attack against the target. Splash weapons require no weapon proficiency, so you don’t take the -4 nonproficiency penalty.
That being said, the rules on
masterwork weapons state that any normal weapon can be made masterwork, and gives the 1/50th cost breakdown for individual pieces of ammunition (6gp per item):
A masterwork weapon is a finely crafted version of a normal weapon. Wielding it provides a +1 enhancement bonus on attack rolls.
You can’t add the masterwork quality to a weapon after it is created; it must be crafted as a masterwork weapon (see the Craft skill). The masterwork quality adds 300 gp to the cost of a normal weapon (or 6 gp to the cost of a single unit of ammunition). Adding the masterwork quality to a double weapon costs twice the normal increase (+600 gp).
The
Craft skill tell you what you can make masterwork. So, if acid flasks are spash weapons that count as weapons, then supposedly, they could qualify under the Craft skill as being weapons that could be made masterwork.
Creating Masterwork Items
You can make a masterwork item—a weapon, suit of armor, shield, or tool that conveys a bonus on its use through its exceptional craftsmanship, not through being magical. To create a masterwork item, you create the masterwork component as if it were a separate item in addition to the standard item. The masterwork component has its own price (300 gp for a weapon or 150 gp for a suit of armor or a shield) and a Craft DC of 20. Once both the standard component and the masterwork component are completed, the masterwork item is finished. Note: The cost you pay for the masterwork component is one-third of the given amount, just as it is for the cost in raw materials.
TL;DR: In the most RAW sense of the word, yes, I think you can make masterwork spash weapons, although don't be surprised if your DM says no. Splash weapons have often been a point of contention (see flask rogues).
