In this case, it is easier to summarize the halachic sources than to give an absolute ruling.
The gemara[1] derives from the mitzva to stand up for a talmid chacham that it must certainly be required to stand up for a sefer Torah. The Shulchan Aruch[2] rules that this is relevant only when the sefer Torah is being moved before the people. When it is out of sight or has been placed at its destination, one may sit. This is derived[3] from the Torah’s mention that Bnei Yisrael stood for Moshe until he entered the ohel mo’ed.[4] Since the law of standing before a sefer Torah is derived from standing before talmidei chachamim, the obligation does not exceed that in place regarding Moshe. Thus, when the sifrei Torah are stationary in their special place (the aron kodesh), the Torah law to stand for them does not apply, even if they are visible.
Furthermore, the Rama[5] rules that when a sefer Torah is resting on the bima, one need not stand because it is in a separate domain from that of the people. The Taz[6] comments that when the sifrei Torah are contained within the domain of the aron, it should similarly not be required to stand for them. However, he points out that the minhag is to nevertheless stand in their honor when the aron is open.
Some minhagim turn into binding practices, whereas others do not. Rav Moshe Feinstein[7] wonders whether the Taz is claiming that standing when the aron kodesh is open is a minhag that became a binding halacha or one that remained a positive, voluntary practice. He prefers the reading of the Taz that it is a voluntary practice. This would be the case if those who began the practice did not institute it formally, as future generations are expected to continue a practice with the same level of obligation that their predecessors did. Rav Feinstein points out that even if there is a doubt regarding which type of minhag it is, one can decide the matter leniently. The Panim Me’irot[8] has a somewhat stricter outlook, and even Rav Moshe urges (without outright requiring) a rare community that sits before an open aron kodesh to conform to the prevalent custom.
Nevertheless, the different approaches to the practice of standing before an open aron kodesh are still significant. If the minhag is binding, the obligation fundamentally applies to all. Of course, even when all are obligated, some are not physically capable of complying. For example, someone who is recuperating from knee surgery may sit even for Kedusha, despite the fact that halacha normally requires standing. However, when it is only uncomfortable to stand, one must do so when it is required. If the minhag is not binding per se, one can consider other factors more liberally and evade compliance due to moderate discomfort or if it compromises his concentration, etc.[9] Admittedly, it is difficult to give absolute guidelines. However, if we agree with Rav Feinstein’s assumption above, as we do, there is more leeway in considering personal needs as a deciding factor.
The Aruch HaShulchan’s[10] formulation puts the matter in a perspective with which we identify. After explaining that the halacha does not require us to stand before an open aron kodesh, he writes: “Since [people] developed the practice to do so to honor the Torah, it follows that one who does not stand in effect shows a lack of honor for the Torah. It follows that it is necessary to stand. However, if someone has weak legs and people will not suspect him [of disrespect], it is permitted to sit.”
Based on all the above, we suggest as follows. On Yom Kippur, and especially during Ne’ilah, we should try our utmost to act properly and certainly avoid anything that could be misconstrued as being disrespectful to the Torah. However, people are aware that many fellow congregants are physically spent and find it extremely difficult to stand for long stretches of time. Therefore, it is permitted for someone in that category to sit. Nevertheless, if one feels that his sitting will be misunderstood or will adversely affect others, he should find a couple of minutes when he will not be missing critical sections of the tefilla to step out of shul and sit. In that way, he can regain his strength and continue davening and standing.