To be exact, Swastikas are not illegal in EU, just some countries like Germany and Hungary. There have been proposals for a EU-wide ban, but they've been dropped.
I've seen those too. Some manufacturers have swastikas on box art but have multi-part decals or none at all. Some don't show the markings on the boxes, but include full decals. At least Hasegawa and Eduard seem to have sheets with full swastikas on the side for easy removal when sold in Germany for example.
Talking of swastikas, I've heard stories from fellow modelers buying WW2 luftwaffe kits from German webstores and upon opening the boxes, finding the decal sheets censored with a black marker pen. Made a mental note of that: "don't buy Luftwaffe kits including swastika decals from Germany."
Sorry, going a bit OT here...