What is the punishment if the employer put a fake signature on the employee work permit?

Prison. But the problem is proving that he is the one who forged the signature.

The punishment can either be imprisonment or a fine of not less than UAE Dirhams five hundred but not exceeding UAE Dirhams two thousand or both imprisonment and the imposition of a fine.

As per Article 1 of the Law of Evidence, the plaintiff has the burden of proof for his right and the defendant must disprove it.