Yeah I knew about this months after I came back into WL4 after last playing it for years or just researched it a long while ago, that certain items do certain damage and the biggest weakness based on boss yadda yadda. By default, new players assume that it'll deal more damage the more expensive something is... which is partially true, but what about the 4 items that are ESSENTIALLY the same price, but deal different damage? Yeah that will require the new players to research that themselves. The only item I know by heart based on this research is that the Aerodant's biggest weakness is the big lips. Idk WHY that is, but everything else I can't seem to remember by heart and I would have to go back and search it.
According to the wiki, it makes perfect sense why Catbat's weakness is the dog, and MAYBE Cuckoo's weakness is the big fist, considering it is a machine that could be broken by human hands, but Cractus' weakness is the dragon??? Well I guess because flowers can burn easily.... but other than that, WHY? As for the Golden Diva, makes sense why the dog is the weakness cause I guess she likes cats, considering she sucks up the cats, but hates the dog, causing it to have the most damage??? Just a guess. Now I have no idea why the Bugle would be the Spoiled Rotten's weakness. I have no clue as to why this is. There isn't much detail to that... thing... that I could form a hypothesis about.
But regardless, yeah those are my thoughts about the Item Shop and why each boss' weakness are as follows.