First off, I am of the definite opinion that spas and pools and other bodies of water you are going to allow your and your loved ones bodies to be immersed in is NOT THE TIME FOR AMATEUR HOUR. If you don't know Art. 680 well enough, you shouldn't be doing it.

The biggest problem with running the conduit directly into the spa is that would imply the lack of the proper maintenance disconnect. The home centers sell a $100 disconnect box that holds a 50 or 60A GFCI breaker inside it. You'll find that often ends up being a cheaper and more convenient solution.

Im sorry I didn't mention that I do have a 50 Amp GFCI spa disconnect panel mounted on the back of the house 10' away from and within sight of the spa. The run I was asking about was from the disconnect box to the spa, since the disconnect box needs to be at least 5' away from the spa. 10' per my local code. As my deck butts up to the house, I would run solid conduit down the wall from the spa disconnect box through the deck and along the joist to the spa. My question was really about whether or not I can run the conduit along the joist since it is so low to the ground or if I need to remove some of the decking and bury the conduit which will be no easy task.

The disconnect does NOT need to be five feet from the spa. I can't vouch for local codes. The maintenance disconnect needs to be within sight of the person working on the equipment. The thing that needs to be five feet away is the EMERGENCY STOP for the motors. This, as far as the NEC is concerned, is not a requirement for single family home spa installations. Depending on what sort of stop you use, it may or may not qualify as the disconnect (or vice versa).

As for the conduit, you can run it as you describe. If it's exposed to sunlight, make sure you get something rated for such. I'd run wet rated conductors in it though.

The best bet is use liquid seal-tite (outdoor flex conduit) and adapt to ridgid for any penetrations.