A hammer is an industrial tool, throwing axes not much purpose in caves.
Hammers are tools that can be used as weapons, but axes and machetes are originally tools that branched out as weapons as well, and machetes, despite having lost a lot of their intended utility Post-Descent, are still very much around as a weapon. Going by the same logic, throwing axes have as much or as little right to be in Underrail as throwing knives, because neither is a tool nor a conventional - or comparatively effective - weapon, not to mention that throwing axes are arguably more historically represented in actual combat than throwing knives (tomahawks & franciscas, namely).