I did the hull/deck joint on one side of my boat last year and it made a big difference. I'm doing the other side this year.
The quantity of work to do this depends a lot on how the hull/deck joint is assembled on your boat. I think my boat has it about as easy as is possible. We have an outward flange as shown here, although it has a teak toe rail instead of aluminum:
In addition to the parts shown there my boat has a rub rail which goes in between the teak and deck (that is held down by the primary bolts) and a decorative cover underneath.
Disassembling the hull/deck joint was pretty easy. First I had to remove the lower cover, which was held on by about 30 #10 screws. Then I had to remove the 3 teak toe rails, each held on by about 15 #14 screws. Finally I removed the rub strip which was held on by 5/16" bolts on roughly 6" centers. These bolts also held the hull and deck together. I put about half of those bolts back in to keep the hull and deck lined up. This is what it looked like as it came apart:
You can see a lot of the hardware spread out on my dock here:
Once apart I removed the existing bedding compound. The perfect tool for this is a Fein multi-tool or one of it's clones.
I rebedded with 5200. It took at least one tube of caulk to do one side of the boat. I would never use 5200 anywhere else on the boat, but I feel like this is a good application for a permanent bedding compound.
While the toe rails were apart I sanded and refinished them.
It looks nice all put back together (image at the end), but more importantly that side of the boat doesn't leak at all. I can't way to to do it to the other side.