Yes, Books-A-Million offers comics. You can find both mainstream and indie comics there. However, it's a good idea to check their online store or call your local branch to see exactly what's in stock.
Barnes and Noble does carry comics. They usually have popular titles and some indie ones. But it's best to check your local store or their website to see the exact inventory they have at any given time.
In Fallout 4, carrying comics is completely optional. It doesn't affect the main quests or your progress through the game. They're more like collectibles for those interested in the lore or for decoration in your settlements.
It depends. Newbury Comics may have foreign records, but it's not guaranteed. They stock based on availability and customer demand. Sometimes you might get lucky and find some rare imports, but other times the selection might be more limited.
I don't know for certain. Tate's Comics' stock changes frequently. Maybe they do, maybe they don't. It's best to contact them or visit the store to see if Yu-Gi-Oh is available.