The simple answer to your 'wrongly' exclude Northern ireland. is YES.
Shopify don't have the UK divided into countries, England, Scotland, Wales, Northern Ireland. So if you exclude one you exclude them all.
I thought you might be able to use UK postcodes or counties, to seperate the different countries, but no.
I am in the Republic of Ireland and I had the same problem. I have stopped sales of certain items to UK for the moment, but it also excludes Northern Ireland. Another example of this problem is the Irish postal service (An Post) offers the same rate for the whole island of Ireland but I have to lump Northern Ireland into the same shipping rate as UK, which is dearer.
Now that we have Brexit and the customs line in the Irish Sea, maybe it's time Shopify addressed this problem.