Update: Thanks to Rob's comment about Davide's answer, I realized I forgot that I had changed my MathJax renderer from the default "HTML-CSS" to "Common HTML" a few days ago. Although this change fixed my issue with the bottom of some equations being cut off, it caused the problem with longer MathJax equations I describe below. With the default renderer of "HTML-CSS" being used instead, the equations are now shown in scrollable windows, such as the Prove that $n$ and $n + k$ are both primes if and only if $(k!)^2[(n - 1)! + 1] + n(k! - 1)(k - 1)! \equiv 0 \mod n(n + k)$. post I mention in my original question text:
Note I haven't tried any of the other math renderer options, or know if using "Common HTML" is supposed to not have the problem of being cut on the right side when it's too long. For anybody interested, I'm leaving my original question text below.
In the past, I've seen both for my own posts and other posts, when a MathJax display (i.e., one surrounded by $$ on either side) equation was too long to fit in its display area, it would be shown in a scrollable window, with a horizontal scroll bar at the bottom, so you can see the left part and scroll the window to see the rest if so desired. However, I noticed recently that this does not appear to be happening any more. For example, with Prove that $n$ and $n + k$ are both primes if and only if $(k!)^2[(n - 1)! + 1] + n(k! - 1)(k - 1)! \equiv 0 \mod n(n + k)$., shown in a full window on my monitor at 1280 x 1024 resolution, I see
However, when I make the display somewhat smaller, I then see this
Some of the equations are now cut off on the right side under the "Featured on Meta" or "Hot Meta Posts" sections, and one equation overwrites the white space just above the "Hot Network Questions" section.
For this particular question, I can just use the full screen. However, there were 2 questions I saw earlier today, but I don't recall which ones now, where even at full screen size they had equations being cut off. Although I could have tried changing my display to use a higher resolution and/or landscape mode, I wasn't sure if that would be sufficient. Instead, I just displayed the question in the editor to see the MathJax code of the non-visible parts.
Note this same issue also applies to longer equations being used in answers, and I believe it's not just on the Math SE site but is also a problem with any site using MathJax. Also, I suspect this issue is due to a relatively recent change related to handling responsive design, with it possibly even affecting other parts of the posts' display than just longer MathJax equations.