Without reading the various federal statutes cited by the Governor in his emergency order granting the National Guard the power to do this, I'll suppose that he really does have this authority, and that it's been on the books for a long time. Either way, with present forecasts of 180 MPH winds headed for the territory, and the history of looting on the islands after previous catastrophes, disarming the law-abiding citizenry strikes me as foolish.
And it is only the law-abiding citizens: those who purchased guns from federally licensed dealers, from whom the authorities will have weapons to seize. The bad guys — and the Virgin Islands have a quite a few of them — will be under the radar.
My guess is that this part of the emergency order will never be acted on but if it is, I'd look for a huge drop in (reported) gun sales as those who wish to protect their homes and families will seek "alternative sources" to buy supplemental, untraceable weapons.
(Almost) all of my various guns have been purchased legally, so state, local, and federal authorities know exactly where they are (a few rare exceptions, also legal, were inherited, or purchased from private individuals back when such purchases were permitted). I'd hate to think that a couple of armed soldiers could appear at my door and leave me defenseless. That sounds wildly paranoid, but these days, who knows?