We have about 3"s of concrete in one part of our shop and we have 3 3016's that will be moved there. Is this too thin for our machines?

yes, get a big steel plate and put it down, or get enough 2 to 3 foot square plates to match the leveling screws.

I've seen 3" even 4" cement crack from just sitting on the 2" x 2" levelling pads due to vibration of cutting, now granted the concrete was typical house concrete not the higher strength commercial concrete.
Also alot has to do with whats under the concrete, if its tight packed and even it works much better. most people when building a building don't tightly pack it and keep it even.

Hmmm steel plates I didnt think about that. I am very afraid we will hae to tear out the floor. I hope this isnt the case but a couple holes must be drilled to check.