If an item can be bought in a shop is it guaranteed to be available for purchase in the catalog?
Yes, the Nooklings store will never sell any furniture item that you cannot order via a catalog. Similarly all items in the Able Sisters shop can be ordered, even "Nintendo" items from them like the Lil' Bro's Hat.
Also note that items found in balloons are often unique; the "balloon" set cannot be ordered from Nooklings' either, just "normal" furniture items (if balloons even still drop that stuff). When in doubt you can always check the catalog itself, it will say "Not For Sale".