The software to link will depend on repeater, linking type, and edge network access. You still have not settled on a deployable radio network type, so trying to decide specific software is premature.
You would not deploy a portable tower in a hurricane, only after and usually near a base or other staging area where there is fuel/security/routes in and out. You would deploy a portable tower in a flood typically at the edge of the disaster. You would not normally drag a tower through flood waters. The tower could then be repositioned as the "edge" of the disaster shifts OR you could deploy additional portable towers with microwave or satellite (VSAT or MSAT) link back to the original tower.
In the work I have done with the Federal Govt, they liked to build a BOO (Base of Operations) at a distance where you could put your thumb over the entire disaster area (i.e. when it was fully extended from your body it would completely cover the disaster). This isn't always possible. In my experience, the guy with the best logistics (including comms) is often the most successful. So, much of the technical feasibility of these solutions is going to be based on what your response looks like, what logistics you will have available, how simple it needs to be to deploy, and what the budget will be.
Since we are talking basically a big flash mob of boats, this will require some special sauce. TT