Best way to process accelerometer data (floats, Float32Array)?

Unfortunately the FPU isn't really used, no.

The issue is that the JavaScript says that basically all maths should be done using double - so there are very few points where floats can be used - and it makes very little sense to include two sets of maths functions for float and double in such a constrained device.

Realistically you'll find that if you're using JS the execution overhead of JS is far greater than that of dealing with doubles, so your issue is what makes the most efficient use of memory (and for that, Int16Array wins).