The actual defence to be taken by an accused comes out only when the case is being proceeded with. However, a complainant has to prove the following to succeed in a complaint of cheque bounce:
(i) Cheque was issued against legally enforceable debt or liability,
(ii) It was presented for payment within its validity period (6 months),
(iii) It was dishonoured for want of sufficient funds, exceeds arrangement etc.
(iv) statutory notice in writing within one month of receipt of information of cheque bounce is served on the correct address of the drawer (here your employer),
(v) the drawer fails to make payment of the cheque amount within 15 days of the receipt of the notice, and
(vi) the case(complaint) is filed within one month after the expiry of 15 days' period given to him for making payment.
So you may guess in your facts and circumstances what defences, your employer may take.
Regarding not appearing on medical grounds, the courts have sufficient powers to enforce attendance by summoning through bailable warrants and warrants of arrest if you assist the court officials in getting the summons served.
Besides filing criminal complaint for prosecution and punishing him for his criminal acts, you may also file a suit for recovery of your due amount. You may also get compensation in the criminal case.