Your best bet in this case is to contact the local inspector, since this situation may be open to interpretation. The most fitting code states:

National Electrical Code 2008

ARTICLE 314 Outlet, Device, Pull, and Junction Boxes; Conduit Bodies; Fittings; and Handhole Enclosures

314.29 Boxes, Conduit Bodies, and Handhole Enclosures to Be Accessible. Boxes, conduit bodies, and handhole enclosures shall be installed so that the wiring contained in them can be rendered accessible without removing any part of the building or, in underground circuits, without excavating sidewalks, paving, earth, or other substance that is to be used to establish the finished grade.

Exception: Listed boxes and handhole enclosures shall be permitted where covered by gravel, light aggregate, or noncohesive granulated soil if their location is effectively identified and accessible for excavation.

Article 100 Definitions

Accessible (as applied to wiring methods). Capable of being removed or exposed without damaging the building structure or finish or not permanently closed in by the structure or finish of the building.

It may or may not be acceptable, depending on if the inspector considers insulation "part of the building".

If you do end up covering the boxes, it might be a nice idea to mark/flag them in some way. This way you; or any other future owner, will be able to locate them later if need be.

As far as I know junction boxes are ok for closets. Your local jurisdiction may have other ideas. Please consider consulting them.

Today's circuit panels are full of (expensive) AFCI breakers that will be damaged by flooding and running many wires can get expensive with current copper prices. Could you instead run a heavier gauge wire to a subpanel located above the water line and nearer to the loads, and branch out from there?

Also using junctions to "split" a circuit to go two directions should be used sparingly. Most electricians will expect wiring to "daisy chain" from point to point, junctions can make fault tracing much more difficult. Some jurisdictions require that the wire be unbroken from the panel to the first load.