Just becasue it isn't new doesn't make it right.
And it isn't the notion of meeting with an ambassador in an official capacity that is the problem - I can see plenty of reasons why a meeting between an executive member of a devolved body would be completely appropriate - e.g. to discuss trade, or tourism, or cultural links. The point is that the purpose of the meeting should sit within the devolved responsibilities of that body. In this case it doesn't appear to be.
I didn't say it was right but if it started many years ago then it's been accepted by the UK govt by habit and repute.
As to restricting the meetings, imagine the meeting had been primarily to discuss an inward investment, if there is no chance to consider possible human rights violations of the investing govt, that seems problematic to the decision. I don't think the devolution settlement rules out such consideration or expressing it in such meetings, and as already covered it hadn't been stopped in the past.