I'd imagine there would be some impact on the native ecosystem. You can't prevent the seed from escaping the aquafarm and (potentially invasive) oysters and kelps growing where they normally would not, displacing local species.

That said.. the small footprint of these farms means you could probably localize this impact, or pick areas that are at a lower risk for farming.

Potentially the biggest hurdle here would be regulatory issues to prevent the above issues from happening without stifling the industry.

Super interesting subject.