if it goes to court, then they will simply take the facts into consideration.
you word against his wont mean much unless theirs independant witness statements.
1. the substrate prep isn't to british
standards.
2. the joiner did this part of the work, not you.
3. insufficient adhesive & 4mm tolerence is the tilers accountability
4. a structural engineer should have produced calculations to prove the joists could take the weight of the ply, tiles, adhesive and self levelling compound...this is down to the contractor because as you said, you are a tiler not an structural engineer.
5. the sds drills vibration could have caused vibration impact damage along a section of the tiles or the movement in the floor could have had the same result (an engineer could deduce whats caused the cracks)
just get as much info as possible together and be honest and stick to your version of accounts and thats all you can do.
definately get in touch with a solicitor asap because they will know the score on what appropriate action to take.
best of luck ;0)
ed