1. In the real life militaries of today, can a subordinate demand of a superior officer that they put an order in writing if they feel that the order is to do something questionable
Well, in this case, it's not just questionable - it's flat out illegal. IIRC, biomimetic gel is banned in the Federation. Since Sisko was ordering Bashir to prepare an illegal substance, I would think Bashir would be within his rights to ask something like this. At the very least, the likelihood that Bashir could ask Sisko for 'in writing' would be less important than the fact that Bashir was being ordered to violate the law.