The short answer is "obviously yes". A sea-level launch accepts an additional penalty from the atmosphere. This has several very serious impacts:
- Limits the minimum economic payload, and thus, minimum cost of the gun itself
- Demands that you use an ablative heat shield
- Requires more delta-v from the rocket because of drag losses
The more difficult thing to explain is why someone might think the benefits of sea launch to outweigh the detriments in the first place. In Dr. Hunter's talks he mentions that you'll get sag if you built this device above ground.
It's obviously important to keep in mind that this gun is 1 km in length. It seems pretty clear that you would have this supported at a large number of different places if built above-ground. The sag is then only something that happens between supports, but adding supports also adds cost. Not only that, but you will likely need adjustment at various supports in order to keep the laser-accurate alignment. Other people have pointed out that building a gun on the side of a mountain will help, but if you're looking for a 1 km segment, you've limited yourself to only a handful of potential sites throughout the globe. Also, since the characteristic height of Earth's atmosphere is on the order of 8 km, it's difficult to find a practical mountain high enough to decrease the initial air pressure more than 20%. 20,000 feet would bring that down by nearly 50%, but how many mountains have a smooth 1 km stretch, are above 20,000 feet, and are accessible for heavy trucks? Most South American nations don't even have a mountain of that altitude. Land rights for such a scarce geographic commodity are obviously a major hurtle.
It's not the case that a higher altitude launch wouldn't need an ablative heat shield, but the challenges would be reduced. Also, the alignment issue favors the sea launch in several ways. After all, the benefit of higher altitude launches is smaller payloads, this will likely make the tolerances for alignment more strict.
Economically, sea launch is also vastly easier to service and has some synergy with shipyards, which might be where the tubes are produced anyway. If you can order tubes with twice the diameter in exchange for avoiding more permitting, sagging, and a political minefield, you'll definitely give it serious consideration.