No problem!
You'll be alerted by radio about when countries declare war on Germany. From then on, you may attack their ships without penalty. You'll get rewarded even.
As to mods, I don't have many installed, but I do recommend GWX 3. It adds a lot when it comes to realism, plus many other improvements. It comes with a manual as thick as a book. It will increase your load times drastically and you'll need a fairly hefty PC, but any current gaming rig should be able to handle it nicely.