Can I use "Is it having been sent" for question? I know I can ask "is it sent", that's why, I thought that I can put "having been sent" instead of "sent". Is it correct?
Not in British (or, I think, American) English.
[It is possible that it works in Indian English - I'm only guessing, but I know that Indian English makes more use of progressive forms than other varieties. None of the corpora I've consulted have any examples, for India or elsewhere, so I may be wrong.]
The normal way to express this would be "Has it been sent?"
"Is it sent?" is possible, but unusual.