What makes it interesting for Boris is when the SNP submit a Bill to the Scottish Parliament for a Second Scottish Independence Referendum and it passes.
To be honest it isn't that interesting, because the government has made it clear they will not grant consent to another referendum (at least for several years). He has the law on his side, so holds all the cards.
The SNP is planning to push forward legislation for an "advisory" referendum that they would then use as leverage to negotiate with Downing Street. They think it's a clever way to get around the fact the UK's constitutional position is a reserved matter. However, all referenda are advisory except in very unique circumstances where the law has been changed subject to a successful referendum.
It is 99.9% certain that the Supreme Court will hold the Scottish Parliament does not have the power to hold a referendum on Scotland's independence without authorisation from the UK government.
Or hold the Referendum even when Boris says No.
If the SNP hold a referendum on a reserved matter and they lose in the Supreme Court, they will be breaking the law, and the Scottish courts would be obliged to follow a decision from the Supreme Court. That could mean injunctions against the referendum taking place.
There is a significant amount of "soft" independence support that doesn't want a violent or destructive split from the union. If the SNP tried to push forward with an illegal referendum it would harm the nationalist movement.
Also, if the SNP did push ahead with an unlawful referendum and the Scottish judiciary chickened out and declined to enforce the Supreme Court's decision, unionists would probably boycott it, resulting in low turnout, and the UK government would ignore it. It has been argued that would be "unthinkable" because it would make relations between Scottish nationalists and the UK worse, but relations are already rock-bottom - they realistically cannot get worse.
So, in short, I'm not sure how serious the SNP are about breaking the law. I think it's more likely they will try it on and then go away and grumble for a while if/when they lose the case.
WRT the RN if that came to pass, that would mean them losing their nuclear sub base at Faslane which would have to be relocated to England and a significant sum expended cleaning up the base. The RAF would also lose Lossiemouth as well where the P-8A is to be based. The RN shipbuilding would have to be moved to English yards because Northern Ireland and Wales continuation in the Union would also have to be queried as well, especially if Scotland gains its independence.
I don't know how much the UK cares about Lossiemouth in the long run to make a fuss over it. However, I doubt Faslane would be closed. Either a lease would be agreed with Scotland or the UK would make it part of the withdrawal agreement that it was to remain in UK hands after independence.
The Act of Union contains no mechanism for Scotland to leave, so even if it was agreed it could leave in principle, if the SNP make demands that are grossly unreasonable it may be that it's told if it won't reverse course it wouldn't be allowed to leave - Scotland cannot leave the UK until an Act of Parliament is passed to allow that.