This is an example of a misinformed TA. First prepaid service charges are refunded if the cruise is canceled for any reason and second people pay many fees prior ro sailing and after final payment and there are no issues. If there were issues with payments after final payment date you can be sure the boards would be all over it.This sounds like a lazy TA issue more than anything.
Since you are before final payment call NCL and they will adjust the price (if they cancel and rebook it shouldn’t matter to you). You can do this as often as you want before you are in penalty phase.
Amber Cove can only host 2 ships, the other two are scheduled for Puertp Plata, cruisemapper doesn't differentiate between the two, it just lumps them together.
Cruising on any given line is a choice. If you don't like what a cruise line is doing with charges, then pick a different one. They all do the same things but don't let that influence your decision.
Getting to Jost from St. Thomas can be done but it is not easy you have to have passport and clear customs and immigration both ways. In addition it is a pretty long ride. The ferries don't go to White Bay on Jost but into "town" so you would then have to walk over the hill or get a cab to Soggy Dollar.
Your best bet would be to charter a boat from Tortola and go that way.
You maybe able to get an upgrade, but the price of your cabin has not decreased so there is nothing to reduce. your best bet will be to upgrade to a higher category cabin that costs more than you paid and pay the difference.