I’m not familiar with this website but I think it just gives you the % of unique words in the DB which have a specific reading. For instance if you look at 挨 on ichi.moe it tells you that it has a single match, probably because it only knows of one word with this kanji, the relatively common 挨拶.
On the other hand if you look at 何 it tells you that the カ reading is used 7% of the time and なに only 26% which is laughable. JPDB and kakimashou have much more reasonable stats with カ at 0%, which makes sense since I can only think of one semi-common word using this reading: 幾何学 (geometry).
So ichi.moe is fairly useless for these stats.
Generally speaking I wouldn’t rely on these types of stats to decide which reading to learn, instead it may be better to look at high-frequency words containing the kanji and then look at what readings they tend to use. For instance the サッ reading of 早 is quite useful but only for one very common word, 早速, so you’re probably better off learning this specific word on its own rather than memorizing a サッ reading on the kanji alone.