You can see the hammer through the bars, but you can't break bars until you have it. The way in is from above: raise the water, swim to the far end of the tunnel, then climb along the ceiling pipes and drop into the room.
How do you solve the water puzzle in Deep Dish Dungeon?
The handwheels raise and lower the water. Set it so the water is up on the far side of the hammer gate, away from where you came in, then swim through.
Turn the handwheel
Walk up to the wheel and press E on the HANDWHEEL prompt.

Swim to the far end
Swim along the tunnel to the ledge at the opposite end. Eels live in this water and hit hard, so don't hang around.
Turn the wheel before you jump in. If you swim first and change the water later, you end up on the wrong side.
How do you get the hammer behind the bars?
From the far end of the water tunnel, climb onto the pipes and follow them back over the bars.
Get onto the pipe
At the far end there's a pipe running back the way you came. Jump onto it; you may need to crouch.
Walk the pipes
Follow the pipe to the wall and look up: there's an alcove you can jump into. From there it's crouch-jumps onto ledges and crouch-walking along the pipes, which works fine solo.
Drop into the hammer room
Keep going until you're above the room, then drop down and grab the hammer. Have a free slot ready, because there's more loot down there, including leather.
How do you break rusty bars in Deep Dish Dungeon?
With the hammer. It smashes rusty metal bars and fences, so once you have it, go back to every barred gap you couldn't get through.

The hammer opens new paths near the water and upstairs. It won't help with roots, though; for those see how to cut roots.
Where do you find the second small key?
Small keys get used up when you open a door, so the first one disappears from your inventory. The second one is at the end of the scorpion area.
- Go upstairs to the second camp area.
- Take the collapsed section on the left and follow the hallway to the end.
- Kill the two scorpions there.
- The key is on a hook on the far side of the pit room.
That key opens the high door across the gap in the hub room.
Should you bring a torch for the hammer route?
Yes. The pipes and tunnels are close to pitch black without one. It does take up a slot, so empty something else before you head in.