I'd look at a laser cutter for making those things, rather than a CNC router. A 1/16" cutter is pretty fragile, so you won't be able to cut as fast as you might like. There's the dust issue, and holding down the parts to consider (as you're doing), which isn't an insoluble problem but does add complication. You can mask off the porous spoilboard to concentrate the vacuum where it's needed, but tabs would still be a good idea if you're using the router - not needed if you're laser cutting.
If it's 1/8" MDF, what gets it up to .145" ?