Arelith

With a single deity (K&I/T&D) I get piety from crafting and stealth. When I add an attuned deity (War/H&H I think?) I appear to get piety only from the second deity's aspects. Removing the attuned deity gets me my piety-gain back from my main god. Is this intentional?

Yes. The primary attribute of the lesser god replaces the secondary attribute of the primary god when attuned to a Main Deity and a Lesser deity.