I've spent a lot of time re-texturing some purchased models in Houdini for use with Arnold materials. However, now it's dawned on me that some of the FBX models that imported with a scene level node with various “object” parts linked together can't be instanced and manipulated as the objects level models can. Is there any trick that can reduce these finished models to a single object with materials intact?

The Combine shelf tool, under Modify will do that. The materials should be applied via a material node. not at scene level.

You can then write out the combined geo as .bgeo and that should instance*

*Not tested but should work.