It's also possible it has floated to the surface and they can't locate it because it's very hard to see when surfaced.

That sub has melt away ballast connections. The attachments to what allows the sub to sink will melt away after 8? hours. So it may have floated back up.

Problem is they are bolted in from the outside and they have no communications working.

I read an account that a person standing on the recovery ship, could not pick out the sub when it was right next to the ship. It sits so low in the water with barely anything above the surface.

Water absorbs electromagnetic signals (at some point, including light). That's why the only really effective way to look for something under water is sonar (loud sound/pressure waves), and even that has a limited range. That, together with the ocean being so big, is why military submarines can hide so effectively.

A radio transmitter or radio beacon on board of the submarine wouldn't work because the water would block the signal. However, the submarine could use a sonar beacon, like the ones used on airplane black boxes. The standard ones have a range of several kilometers, but there are low-frequency ones that transmit pulses at 8.8 kHz with a range of 10-30 km (search for "8.8 kHz beacon"). The answer why they don't use that seems to be simple: They don't have it. - why they didn't install it is a good question. The beacons are able to handle the depth too.

One problem with underwater sonar can be layers of water that have different densities (e.g. due to being saltier and/or warmer/colder). Sonar/beacon pulses can be reflected by those, which could possibly make such a beacon less effective.

Short answer: ocean is very big, submersible is very small.

Long answer: Imagine going out on a football pitch with a white paint marker. Randomly walk around and pick a single blade of grass to paint white. Now grab someone that didn't observe you and tell them to find the painted blade of grass. Also tell them they have a limited time, and that you might have pushed the blade of grass doen into the ground.

the ocean is a big, mostly empty place