For example, I want to select a bunch of static mesh assets in UE4, and use Houdini to generate low-res mesh LODs or collisions to overwrite original assets.
Is there any way to do this currently?

The quickest way to do it is to use Python(in UE4), to export your static meshes to FBX. Then run Houdini, process all meshes. Then with python reimport your static meshes with a new file.

I don't think you'll ever get an HDA alone to overwrite the original assets but otherwise that should all be do-able from a single HDA using a multi-parm input, among other techniques. You'll need to make sure the HDA is an object-level one, not SOP, as you need distinct objects generated in UE, not a merged single one.