When you say no Specters are there, do you also mean there are no dead Specters either? The Specter page notes that there is a Specter carcass near the Ninmah Research Lab that can be scanned so long as it hasn't been looted. I'm not sure if its ability to be looted restores itself to ensure there is always another opportunity to scan it, no matter how many times the chance is missed.

So dead one can be scanned too and it will be added to machine's database?

So long as it hasn't been looted yet or has other things that can still be interacted with (such as an attached heavy weapon or a Bellowback's sac), I believe so.

Ok right the articles says Specter carcass while I thought its just "alive" one lol.

But I still find it weird. If Specter Prime is scanned automatically after killing it then why they didn't do the same with Specters. Or maybe they did idk.

I agree, it is weird. :/ If they have changed it, the wiki doesn't seem to have any record of it and I'm not aware of such a change.