两条鱼is actually better than两条鱼，but you know,this is a children poem,to some extent,its intent is to teach children to learn to count numbers easily,so here we use 二 rather than 两。And the short of a comma is meant to make the sentence looked in good order.my English is a little poor,but I hope my answer can help you and if there's some mistakes in my English answer,please let me know.

Actually两条鱼 is better. 二条鱼is weird ,no one says that.摇摇尾巴点点头 & 摇摇尾巴，点点头 are the same thing , but if we omit the" ," the writing will looks in good order and the reading will be smoother.

一、这里说成“二条鱼”并不好。虽然是小孩子的儿歌，依然应该用标准的语言，而不能只管一、二、三这样的形式上的对应。“二”一般只用于单说数字的时候，还有就是特定的词组中。 二、理论上说“摇摇尾巴”的后面是可以加逗号的，但并不一定非要加，尤其是在诗歌中，诗歌可以完全不用标点的。

For the second question, in fact, we don't have standard punctuation in the traditional Chinese essay. So the punctuation we are using now actually comes from other language system like English or some mixed language. But as the poem is a kind of traditional form of literature in China, so the order will be more important. And I guess punctuation in Chinese is not as important as those Western languages, as we have lived through thousands years without it lol.

1. This is a poem, so poetic license is used. Just like in English, the order of things can be written in a weird order. Here, 二 is used to give it a sense of literary refinement. 2. Actually, you are correct in having the comma there if you want to recite it in a classical manner. However, you must do the same for the rest. The pattern is 3 pause 3 on the odd lines and the even lines, 4, pause 3. 一条鱼，水里游， 孤孤单单, 在发愁。 二条鱼，水里游， 摇摇尾巴, 点点头。 三条鱼，水里游， 开开心心, 做朋友。