The Swastika-on-deck thing really wasn't all that widespread- early in the war it was done to keep the Luftwaffe from bombing their own ships by mistake, but only in home waters- once out in the open they'd paint over them. Later on, they weren't done at all, as Allied planes took over the skies. (And really, if you're not comfortable painting that on the miniatures- I know I'm not- an Iron Cross is still very German-feeling without being creepy, and not too far off in shape to be 'inaccurate'.) I know Bismarck had them, and I'm pretty sure at least a couple of the Narvik destroyers did, but I haven't seen anything showing other German ships ever having had them.
OOBs... I mean, Wikipedia isn't the worst place to start, honestly, at least in terms of individual battles. An interesting 'what if' would be Matapan without the Italian cruisers being caught with their pants down. (It's an interesting engagement, if you ever wanted to know what it looks like when an otherwise-reasonable naval force gets absolutely curbstomped by an opponent!) The main problem was Italian commanders preferring to avoid combat, so you didn't end up with a major engagement between the British and Italian fleets outside of skirmishes for the most part. I suggest making your own scenarios in that regard- certainly when it comes to their heavy ships, there's not a lot of heavy action to explore historically.