Usopp only has one bounty. The Marines aren’t morons, they were able to piece together that a big nosed sniper in a mask is the same person as a big nosed sniper without a mask.
In a similar vein, they know that Sanji is a Strawhat and a Vinsmoke, so there’s no reason to think they’ll not be able to piece together that the guy wearing Vinsmoke technology running around with the Strawhats is in fact Sanji.