Are there any differences (nuances or usage) when using prefix 子, 小 or 仔 for denoting young animals?
- Kitten: 子猫 vs 小猫 vs 仔猫
- Puppy: 子犬 vs 小犬 vs 仔犬
- Pony: 子馬 vs 小馬 vs 仔馬
- Calf: 子牛 vs 小牛 vs 仔牛
- Lamb: 子羊 vs 小羊 vs 仔羊
- Piglet: 子豚 vs 小豚 vs 仔豚
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The OP's comment just now is on the right track:
小猫 certainly could be just a small cat.
仔猫 would be more common in science, but for a different reason than you guessed: 仔 is actually the correct character for a child animal, but it's not one of the 1945 -- er, 2136 as of last year, is it? -- 常用漢字. Since 子 looks and means almost the same, it took on the added responsibility of being the simplified form of 仔.
I think for the anthropomorphism case those characters would need to be switched. =p
Google hits [Japanese pages only]:
"仔猫" - 3,160,000
"子猫" - 10,700,000
"小猫" - 1,310,000