-Quest problem> I have no problem with getting items that have little usage after the quest is complete. Zelda does this all the time. Halfway through the quest you get an item you need to complete the other half of the quest. The important part is requiring the item's usage during the quest itself, and not giving the item at the end. Then the end prize can be the hat, bomb skin, whatever. As for using the hammer after the quest; instead of just blocking a few chests, wooden stakes could also block paths to new points of interest that are likely to be visited multiple times (places similar to crab game, Mercator's, etc; and the stakes reappear when you leave the overworld).

-Multiplayer Dungeons> [if this ever happens] Instead of having a party system, i think it would be more appropriate for it to be guild-based. As for the number of participants, allow 2-(whatever maximum you want) to start the dungeon; just design puzzles for a fixed number of people; and each puzzle can be made for a different fixed number of people. If you enter the dungeon with only 2 people, and there's a puzzle that requires 4 people, you'll have to realize this yourself and retry when you have more people. If you have 6 people, and a puzzle for 4; I dont see the problem with 2 people sitting out for one room. Or to have a puzzle made for a variable number of people, have "x" number of people complete the puzzle when everyone else is fighting off enemies from interfering.