With new circuits, a hand full of Wago's should allow a quick test on the full cable run @ 500v prior to fitting the USB accessories. But on EICR, or additions to a circuit that already has USB's scattered around I would do 500v L->E, N->E (or L+N->E). Then L->N @ 250v. Unless I've seen manufactures documentation saying their USB sockets can withstand 500v IR testing I would assume they will be damaged and not test at that voltage. I don't think I would start opening up existing USB accessories to isolate them from testing, to then put them back in circuit afterwards, as I think this is more likely to introduce faults that weren't there before.
On a slight tangent, do these USB sockets have any natural earth leakage via their circuitry? e.g. if you had a lot of them all fed from the same RCD could you get nuisance tripping problems.
Doc H