Is it OK to thank the examiners in the acknowledgements of the final draft of a PhD thesis?
Peer-reviewers of academic research papers are not supposed to be authors' friends, and on many occasions are direct opposite. However, it is not uncommon to thank them in the final version of the paper, because their contribution often helps to improve the paper considerably.

In the same way, I think that it is OK to thank the examiners for their suggestions, which helped you to improve the presentation of your thesis.