Wrong box. Bad installation.
Why is the lid so warped? Far too much stuff was crammed into that box than was legal (cubic inch rules) or practical. So the installer just cranked down the lid screws as best they could, leaving huge gaps. 110.12 violation. Total amateur hour. Amateur hack-installed hot tubs are scary, so I would review the entire thing soup to nuts and look for other violations and shoddy work.
Apart from that, if you're doing a splice you want to keep water out of, why not attach the conduit and to the ceiling of this space (i.e. bottom of deck) so the box is face down? Then any water that gets in the box just falls out through the imperfect seal on the lid.
But use an adequately sized box, for Pete's sake. This box is intended for two 12/2 cables feeding a single light, a hot tub box needs as a bare minimum 25-35 cubic inches depending on if there's a neutral or not. I can peek through the product photo and see where it says "VOL 13" or possibly "15". So half the volume required for the job.
It's not enough to have a square box, you also need one both with the statutory 25-35 cubic inches, and also the practical space needed to hold the splice.
I know the cost of #6 copper is terrifying, but we have answers for that.
I'm not sure what are these "elbows" of which you speak. When dealing with conduit, you must assemble the conduit complete before you pull any wires into it. As such, the conduit must be "pullable". We get people who think "I want to make a 90 so I'll just use a plumbing elbow". You can't pull a wire around that, obviously. You need to either use special corners with access covers (for pulling) called "conduit bodies", or well placed junction boxes acting as a conduit body, or broad curves known as "sweeps".
Also you can't have more than 360 degrees of bend between access points. (which conduit bodies and junction boxes are, fortunately).
What I would do
If I were you, I'd pull the wires out of the pipe from the hot-tub end, then come down that vertical with either a 90 sweep or two 45s (depedning on the geometry) and then run the conduit along the bottom of the deck joists. Feel free to curve the conduit to the extent it is able, no need to "Minecraft" this thing.
By the way, "45" bends are a thing, as are arbitrary bends made by heating the PVC conduit - be careful not to kink it.
Then place a properly sized junction box, like I say, attached to the joists face down. Make splice(s) there. Nothing wrong with having two different splices a few feet apart, but replacing a length of wire run is also fine.