What I'm betting is that the Yeerks called them Pool Ships, and the Animorphs probably interchangeably called them Pool Ships (because that's what the Yeerks called them) and Mother Ships (because of the sci-fi aspect).
After all, Yeerks have no reason to even have a word for "Mother." Yeerks are obviously lacking in the parental aspect, given that they die when they reproduce. And since they have no gender, they would never even need to refer to a 'female parent.'
Even if they did have the word 'mother' it would have an extremely different connotation to them than our word does. To a human, a mother is a being who takes care of you and looks after you and protects you (and it is from this connotation that "Mother Ship" would have to derive). To a Yeerk, a 'mother' is simply a dead Yeerk from which a new generation descended. Nothing more than that.
So I cannot imagine that the Yeerks would consciously name their own ships after something that is such an alien concept to them. Therefore, the term "Mother Ship" would have to have come from humans, at some point. If any Yeerks do call their ships "Mother Ships" it is almost certainly a habit they would have picked up from their hosts, not the official name.