Cool Whip tagging enemies would work, but it shouldn’t be 10 (that’s more than Durendal!) I’d put the tag damage at 7, equal to Spinal Tap and 2 lower than Durendal, for 2 reasons: 1, you have the snowflake and debuff doing damage already, and 2, you don’t want it to be too strong with Blade.
Well the tag damage would replace the snowflake's damage, and the Cool Whip would still have two main disadvantages compared to Durendal: it doesn't give any sort of speed buff, and you can't apply the tag damage directly since it's applied by the snowflake instead. That's why I set it so high, since the disadvantage of being beholden to the snowflake's AI needs something to balance it out. That said, maybe lowering it to 8 or 9 would be better, but I do think 7 is too low.
For Lunar Flare, I’d honestly make it a crowd focused weapon. It’s not that hard to aim - the projectiles are quick and accurate to your cursor, making it pretty focused. The issue is not it being weak, just how much better Last Prism is. I’d make Last Prism a single target beam and keep it from piercing enemies, and then increase the spread and explosion size of Lunar Flare.
It honestly is way too slow to hit targets nearly as reliably as it should. By the time you get it, your main concerns are the Moon Lord and the pillars, and its projectiles are just too slow and narrow to hit either the Moon Lord's eyes or flying pillar enemies with any degree of accuracy. You could nerf the Last Prism, but I'd rather that not happen because of how iconic the Prism is, not to mention that the Lunar Flare would still be outclassed by other weapons like the Celebration Mk2 in everything but wall-piercing.
Gem Hooks being harder to make probably isn’t the optimal solution, people usually want to have a hook asap and locking the gem hooks behind this gate would make them a bit later on. I’d just buff the drop rate of hooks like you said and then buff Grappling Hook, make it a sidegrade rather than downgrade. When Gem Hooks aren’t considered too strong, buffing the other options would be taken much better than nerfing the gem hooks.
Well, part of my concern, albeit a minor one, is that the Hook item is now practically useless since you'll usually have a gem hook by the time it ever drops. What if it were added to the gem hooks' recipes, but the gem requirement were also reduced by something like 5 each? On top of being a more common drop, and maybe even dropping from more enemies. I've noticed that gems tend to spawn in veins of around 10, so making 10 gems + 1 Hook the requirement could actually make grappling hooks easier to craft.
Nano Bullets aren’t completely a poor man’s Chlorophyte: they’ve got better damage, but more importantly, you can buy them. Chlorophyte is a scarce resource and chlorophyte farms are slow, so just being able to buy pseudo-homing outright makes them pretty helpful for when you don’t want to waste Chlorophyte, such as during longer events. Maybe confusion should be temoved from both and Flask of Nanites just needs its own effect altogether, you don’t need Confusion by post-Plantera and it’s often unhelpful.
I've done some testing with both Nano and Chlorophyte Bullets, and Nano really is a poor man's Chloro. The damage debuff after bouncing, on top of the requirement to have blocks nearby to bounce off of, reduces Nano's effective DPS by a lot. In my tests the Nano Bullets were getting like half as much DPS as Chloro, and I like to think I have pretty good aim.
Being able to buy the materials for them is an advantage, but Chlorophyte isn't as rare as you're implying. 1.3 buffed its availability by increasing the amount that can spawn per area, while 1.4.1 eased competition for it by reducing the number of ore per bar, even if Chlorophyte Bullets themselves still take almost the same amount of ore. Not to mention, Nano Bullets are supposed to be a whole tier above Chlorophyte, so there's that to consider.
How is this thing too strong? Here's a few around its tier I'd say are roughly as strong:
A blowpipe using seeds has the same base damage as this thing, and the boomerang can have more/less attack speed depending on distance.
Wand of sparking has roughly the same damage but trades knockback for a pierce.
Poisoned knives are obtained roughly the same way (wood chest item + cheap material), they may be limited as a consumable but they are better than the enchanted boomerang at literally everything else.
Putting a ruby in its recipe means it has to compete with the likes of: gold bow, ruby staff, mace, ice blade, or snowball cannon.
I would say that all these weapons are much more useful than the enchanted boomerang.
All of those weapons you listed for comparison take limited resources to use. The Enchanted Boomerang can be used infinitely. It also has way more knockback than any of those, which is extremely important at the beginning of the game. The cooldown after throwing the boomerang nerfs it somewhat, but it's not enough to keep it from being way more useful overall than any other weapon in its tier, especially if you're fighting close enough to enemies that you can spam it very quickly. And with its massive knockback, there isn't even that much risk to doing exactly that.
I'm not sure how adding a ruby to its recipe would make it compete with the Gold Bow or Ruby Staff, since those require gold bars which are much more difficult to obtain than a single ruby. The Mace, sure, but that's why I said it was a secondary suggestion. I think that just changing the recipe to 1 Mana Crystal and a Wooden Boomerang at an anvil would be enough. Part of the issue is that it's so easy to craft that it makes the Wooden Boomerang obsolete, since you're always just going to upgrade it as soon as you get it. 1 Fallen Star is nothing when they're so common now. At that point you might as well just remove the Wooden Boomerang from the game and put the Enchanted Boomerang in wooden chests instead.