Worth it? I can't say. But basically you're looking at the cost of the bike plus the cost of a wheelset. The bike is a good deal, so no worries there, and the wheelset is a great wheelset, and it costs what it costs, so no worries there either. If the bike turns out to be less than ideal, it's easy to put the original wheels back on it, sell it for $150, and try the new wheelset on a different bike. So... worth it or not worth it, it's not a waste of money.

If you're worried about the brakes, consider getting a Sturmey-Archer drum brake and dynamo combo hub for the front, and you will have excellent brakes and free electricity for aout $50. You can also put a Shimano roller brake on the rear, it's an excellent brake but it's heavy, it rattles, and it's a bit of a pain to take the wheel out of the drops. But no big deal; the standard Nexus hub accepts that brake, but you have to buy the brake seperately; so just add it later if you wish.

Chain ring: good question, you're on the right track but no worries (I think). The nexus hub is designed to work with a 2:1 ratio, chain ring to cog; so 38/19, 40/20, etc. The hub probably comes with a 19 and a 21, and your bike probably comes with a 46, so ideally you want a 23, which is not hard to find. And again, you don't need to do it right away. Wait until you have to order something else, and put the 23T cog in another order.

Threading. Yes, it's true, your Sprite will have 26 tpi Raleigh proprietary threading, so replacing the headset and BB will be tricky. But again, no worries; these things are built to last, and if properly maintained should last longer more or less for ever.