Yes, you should fill any cracks in the slab, before you cover it up. You will need to clean and groove the cracks with an angle grinder with a cement blade. Use wwHenry 549 feather finish to fill it.

It's a good time to level it, before covering it up.

The subfloor can be floated over a vapor barrier or fastened with a vapor barrier adhesive. Fasteners can't puncture through the plywood.

I'm not a fan of putting down plywood over concrete just so you can have a nail-in-place hardwood. Soooo many ways this can (and will) go wrong.

Personally, if you MUST have a wooden subfloor over concrete, please use a sleeper subfloor system built properly with the proper vapour barrier used.

Or in the worst case scenario, something like DriCore (I'm not a big fan, but it will work when done PROPERLY....ahem, I'll say it again, "when done PROPERLY").

You still have to patch the concrete. After that, you can use a vapour barrier (see how you can't get away from that?) then you lay the DriCore panels down and THEN you lay the PLYWOOD over the DriCore....and THEN you nail down the hardwood.

Whew!

Or you can look at engineered floating hardwood over a vapour barrier (there it is again) and a BEAUTIFUL cork underlay....like 1/2" cork would be AMAZING!

As you can see, I will try EVERYTHING I possibly can to AVOID this type of subfloor system you are talking about. And I mean $5000 - $10,000 MORE to get away from it! That's how much I HATE the system you mentioned.

Make sure your builder does everything properly (concrete patch, etc) and offers a LONG warranty on that subfloor system. Like 5-10 years (s/he won't like that ONE BIT). If s/he won't do it, then perhaps you would like to look at a different system.

Shooting nails through your slab wouldn't be a good idea, if, you have known leaks.

Difficult to say.