NextCloud was an independent company well before it did anything government related.

The only thing that's happening here is they appear to have struck a huge contract with a few EU countries to build internal clouds.

I believe NextCloud is open source, and a fork of owncloud from the original owncloud developer who wasn't happy with the direction it was taking, or something like that. Also, they are a profitable company, and the product is open source, so this only looks like a boost to their business model and the open source product it's based on.