It should be noted that the nuclear armoury is based only 15 miles from Scotland's most populous area, the city of Glasgow -- which in the politics of the union is totally fine so long as it's nowhere near English cities. The system has had multiple failures and there have been attempted coverups of accidents at Coulport (where the weapons are stored). The Royal Navy also stores the decrepit and rusting nuclear submarines at Rosyth, a mere 10 miles from Edinburgh, our capital city. Again the thought of storing these at Southampton or Portsmouth would not be considered because it's too close to English who don't want rusting nuclear vessels in their backyard.
Senior MOD officials have been on the back foot in this debate even though most UK military assets have already been removed from Scotland (airbases have been shut and army decimated). Rather like in a divorce where one party tries to remove as many assets as possible before a possible split. The problem with the nuclear armoury is that none of the other areas of the UK want it and it would be political suicide for an English MP to accept into their area.
Scotland, if the vote is YES next month, would be a small country and it would not be right to have nuclear arms. Scotland wants to set an example by not having them on our soil. Scotland has only been invaded by one country in the last 1000 years, it's a country to our south. Scots like the English (this is not an anti-English referendum) - we just don't like the arseholes in Westminster telling us what to do (neither does large areas of England as it happens)
To learn more about the Scottish independence, see The Wee Blue Book