I know Houdini's scene scale default is 1 unit = 1 meter and that it can be changed to be whatever you want but you can run into problems with DOPS and maybe POPS. I am starting a project with cellular and molecular forms and wondering if I need to change the scale to be that small. I'm not concerned too much about scientific accuracy with regard to forces such as gravity, etc at that scale as it would likely be different and I wouldn't know what the accurate equivalent would be in any event. Maybe just change it to millimeters?

I guess the best thing for you would be to find a reference of the motion you want to achieve and try get to that with the normal scale. If you're not concerned about a 100% scientific accuracy, go with a reference and have it to look and feel right. In some cases for simulation work on finger tip scale, it helps to uniform scale everything x10 (or higher) to not have like 0,000x numbers where you loose accuracy because of the many zeros behind the comma (–> 16bit float accuracy).
Most of the times it would work with these small numbers but sometimes it can make things crazy.

But you can try it out to change the unit scale, if it gives the best result, go for it! And it's a good thing to keep the scene scale in mind, mostly when you get models from different software (for example Maya and Max is working in cm)

Thank you David that is helpful to think about.
I will try to find references and guess what might work in terms of visually representing it. Much of what I've seen of the motions of molecules or cellular structures are either too insanely fast for humans to process or it's clearly just invented to better tell the particular story. I will be heavily leaning toward the latter unless told otherwise by a client - right now I'm just making this for my own purposes so I have a lot more leeway and I will be modeling all the imagery myself or importing it from the pdb database - so they will all be consistently at the same scale. I'm tempted to just make the scene scale at 1µm (micrometer) but if that would make everything too weird for Houdini dynamics then maybe I'd just fake it with using a larger scale like 1 mm or 1 cm.