There is no way to tell what will be the final result of a particular fault on a particular horse because each horse will progress differently depending on what they are asked to do, how they are trained, and the individual horse's own body.
If you were looking to do mid to higher levels in some discipline, then I would say yes, you would likely end up with soundness issues simply due to the body stress that higher levels of competition require...but then again, he may be fine even to the highest levels, only time would tell.
All I can really do is say that certain faults tend to predispose a horse to certain conditions. For example, IME horses with small feet, upright pasterns, and straight shoulders are predisposed to having Navicular. That doesn't mean that every horse with those faults will end up with Navicular, but they are predisposed to it. So, given the same care and workload as a well conformed horse, the horse with faults is more likely to end up with it.
Best I can really suggest with your horse is to make sure and let him mature before you start him under saddle and condition him slowly and properly to the level you want him to be. It is possible that he may end up with some sort of soundness issue...but it is also possible that he will be healthy and completely sound for the rest of his life. All you can do is do like the rest of us, regardless of a horse's faults; treat him right, watch for discomfort, and enjoy him.