IMO, enemies becoming HP sponges in endless runs is not fun at all. It invalidates a lot of builds and items except the highest damaging ones (Cleavers, Assassin's Dagger, spikes stacking) and for others that still work it takes way too long to finish a single encounter.
My suggestion is to add items or weapons that let you deal percentage-based HP damage, maybe a gem like Whetstone that upon use makes your weapons deal 1% HP damage to enemies. That would help with the infinite scaling