Here's an example sentence from 北斗の拳 which uses a fair amount of furigana throughout.
xxxに残された命は三日...
Which includes furigana for のこ, いのち, and, bafflingly, even the か of 日, but none for 三. While I already know that 三日 is みっか, there are plenty of other words with numbers that are beyond me. I'm sure I'm not the only student frustrated by this practice. What's the reasoning, if any, for this?
The number kanji are included on the list of first grade kanji that all Japanese children, theoretically, should know by they are in the second grade of elementary school. The other kanji you list (except for 日, but they may not cover that reading) are at higher reading levels. It's likely that they made an editorial decision that, well, pretty much any child who knows the kana well enough to read them fluently is going to know the number kanji at least. The other kanji in grade one - well, they may know the kanji itself, but not necessarily the compound it's in, so I wouldn't be surprised if they furigana'd those as well.
This is similar with bdonlan's answer, but in my understanding,
On first grade, they learned both 三, and 日 kanjis, but only pronounced 日 as "ひ" in "Sun", but not as "か", and also there is some probability that no 日付 related terms learn on first grade like ついたち「一日」、ふつか「二日」、みっか「三日」, ... yet.
So, may be that's the reason why they only put ふりがな on 日, but not on 三.
