I understand the need to use MathJax which I always do but I think it is very inconvenient to keep using it when having small numbers alone in different parts of the text, If I don't use it they look very ugly and bad, for example: 123 vs $123$, in other websites such as stackoverflow they show normally without the need to enclose them with dollar sign
Maths SE uses the font Georgia for ordinary text (not MathJax), as this post says. This typeface has both ascenders and descenders, such as the numbers 3, 4, 5, 7, 9, and in the numbers 6 and 8. This supposedly increases readability in low resolutions, as there is more space that each number fills, but I imagine you are more used to fonts where all the numbers are the same height as each other.
Another point is that Georgia is a serif font, which means that there are small lines attached to the end of each stroke:
In contrast, Stack Overflow uses fonts such as Helvetica and Arial, which are sans-serif. If you mean you prefer the cleaner look of these fonts, then you just might not like serif fonts.