What are the ramification if any if a bank even though closed process inclearing file, ach and system update??

If, by "process," you include handling any returns that result from the inclearings, there should not be any problems. Except, perhaps, some customers who might have been palying it close on balances, and could be caught unawares by the processing of debits only.

returns will not be processed until Monday, from what I gather all inclearing and ach will be processed and posted to accounts and the bank will decide on Monday what to return.