For example for the kanji mother 母 (WaniKani / Kanji / 母) the On-Yomi reading is greyed out.
I think it’s just WaniKani’s way of telling you which is the most common reading.
(Or the reading they want you to input, but the other ones are also valid.)
Yeah, that’s one you’re not going to use for a good long while. I think (coincidentally), I just saw the ぼ reading for the first time on level 32, 祖母. Don’t spend any energy learning that one (yet).
航空母艦 is a cool word.
I believe the grayed-out reading is the one that they don’t teach with the kanji. The one that isn’t grayed-out is the one that they do teach with the kanji. The grayed-out ones still appear in vocab, but they aren’t taught with the kanji itself.