Yeah, it seems like the Baknamy Merchant's inventory is also somehow connected with your Clan Rank just as the Clan Merchant's inventory is.
The Clan Merchant stops selling Hi-Potions quite early on once you reach a certain rank and as you progress through the game and do the hunts.
The Baknamy Merchant could've probably stopped selling ethers at one time in my game as well, but I likely didn't realize it at the time as I didn't check (didn't need them at the time) when I went to him to buy a set of Demon Shields one time.
Many of the shops in this game are overall unpredictable (e.g. certain things not being available until after completing certain parts).