Fishing is one of the most interesting skills in UO because it's core purpose is based on your failure rate, as failures lead to serpents which lead to MIBs (assuming MIB spawner items didn't exist as an option and that was still the only path). Higher fishing does yield a higher chance for receiving rare fish, but I'm not sure the difference matters assuming "fish bait" does the job for you.
Anyhow, the main concern of the OP *should* be addressed by allowing weapon bays on ships a bit more flexibility, as suggested earlier. The problem, of course, is if EA could do it easily, they would have done it. We saw this problem, painfully, when they introduced the captain's wheel, only to reveal this item could only be placed in a house. A real WTF moment in the history of UO buyables. With that concern voiced and addressed to an extent, it wouldn't be too much to ask the devs to push a little further, if possible.
In the meantime:
1) Serpent/Water Ele/Etc corpses are great trash cans
2) UOA offers a Vendor Agent to "Sell All" by type, such as shoes (recall out, recall in)
3) You can exploit the 125 item rule (as long as you manage your weight capacity, a limitation which is frustrating given how heavy "new" fish are) so that everything ends up dropping on your deck
4) You can PK other fishers and then sort their junk
5) You can use the EC's grid mode
Hit or miss. When fishing was introduced, selling shoes--even acquiring them--was useful, since you would die so often and need replacements (although we also had newbified gear, so I guess it wasn't all that important aside from getting a nice pair of boots to go over those bone leggings). Selling fish, as well, was profitable, which surfaced again shortly after people began running quests for the new fish. As a noob, selling cooked fishsteaks became one of my first sources of reliable income, haha, and selling shoes, as well.
I see a few choices. Either you remove the shoes past, say, 100 skill, you add a rarity to the mix to make the process rewarding (and based on skill for proc), or keep it like it is. Maybe a legendary fisher should have a chance at getting some magic shoes, eh?