Essentially answered in the comment, but hopefully the following clarifies your question.
First of all, 常用漢字 is not about simplifying characters and almost never did, except 燈 → 灯.
It is more about which characters are acceptable for official use, and the linked document discusses fluctuations in some characters, including 稽 in your question.
Simplification (in Japanese Kanji context) usually refers to the simplification enforced in 1946, and that is 当用漢字.
Second, on the 旨 and 上+日 relationship, they are called variants (異体字). This does not necessarily mean one is derived from the other, but rather that they are listed as the same character in some old Chinese character dictionary.
So technically any kanji containing 旨 could have its 旨 replaced with 上+日.
That said, I guess 上+日 could be derived from 旨. Because
- as noted in the linked document, 上+日 was conventional in 楷書体 which is the standard style in calligraphy (I mean Chinese calligraphy with brush)
- Straight lines in 上 is easier to write than ヒ.
- FYI 明朝体 is the standard style for printing (with movable types)
Lastly, though probably not the kind of answer you are asking for, but one example where 常用漢字 have more stokes than its variant: 涼 vs 凉.
Also I found the following.
It says 者 was originally without the dot, but later the dotted version was introduced in a Chinese dictionary 説文解字 and made its way into 当用漢字.