My understanding is that the registry is federally mandated, and that basically you have two options. The first is to let/have it under state control, this way you might have some say as to where the eventual fee revenue gets applied. The second is the Feds impose it and the fee revenue goes into the general fund (somebody else's pork barrel). Either way, it's gonna happen.
The feds have to create the database, the $64 question is where do they get the data. They have been instructed ( in the law) to work with states that have a saltwater license to get the data, but, so far, NMFS/NOAA fisheries has said that NONE of the states have a license system that will give them the data they need. If the feds decide to collect thier own data by making anglers register, then it will be (by law) free until 2011. After that it may or may not be free depending on what Congress decides. In any event, the feds can only make you register if you are fishing in federal water, they have no control over what goes on in state waters, and given the fact that you can only fish for stripers in state water nothing they do will affect striper fishing.
As far as the states go, some will probably use this as an excuse to adopt their own saltwater license, some may opt not to and at least one state, RI, cannot impose a saltwater license. what the feds will do when a state can't or elects not to enact a saltwater license is a total unkown at this point.
As for any costs to run the federal system and how they will be recovered after 2011, the feds could impose a fee on all anglers who fish in federal waters, even if they have a state license, or it could be funded out of the general revenue of the U.S. or it could be paid for by an appropriation out of the dingle-johnson sport fishing fund ( paid for by the excise tax on tackle). Those are at least some of the options that will be considered.