We must first investigate the halachic status of a yad.
The Terumat HaDeshen[2] forbids using support rods of the parochet (curtain) of an aron kodesh as “pachim with which to mark the sefer Torah for the obligation of the day,” as this would constitute a depreciation in the status of the objects. The Rama,[3] in accepting this opinion, explains that pachim are “the [pieces of] wood used to mark the sefer Torah …” It appears to me that this refers to tags that some shuls hang on sifrei Torah to indicate which sefer Torah is open to which reading (weekly parasha, Rosh Chodesh, fast day, etc.).[4] The Magen Avraham[5] explains: “They are not for adornment or to dress [the sefer Torah], but rather for a sign that they should not err.” However, he concludes: “But now the practice is to hang them from the sefer Torah for adornment.” In other words, when one hangs such a marker from a sefer Torah in a manner that it is decorative, this use has importance, and therefore one may use the parochet’s support pole for that purpose.[6]
However, the Machatzit HaShekel[7] is unsure whether the Magen Avraham is referring to the tags, as we understand in the Terumat HaDeshen, or whether he refers to a yad. The Pri Megadim[8] and the Mishna Berura[9] understand that the Magen Avraham is indeed referring to a yad. This interpretation works well with the language of the Magen Avraham because he implies that the item in discussion is something that only over time started to be hung on the sefer Torah; a tag would, by its nature, always be hanging from the sefer Torah while in the aron kodesh. It follows, then, that the Magen Avraham maintains that in times when a yad is an adornment that is hung from the sefer, it has the status of noyei kedusha (things that adorn a holy object). Among the halachot of a noy kedusha, which is a form of tashmish kedusha,[10] are the laws that it requires geniza[11] and that it may not be brought into a bathroom.[12]
However, your case may be different. If the yad was never used for hanging on a sefer Torah as an adornment, but rather is always brought by members of the family to use in whatever location necessary and is then taken home, there is no basis to consider it noyei kedusha.[13] We would then apply to it the status that the Terumat HaDeshen and Rama attributed to it – that of a lesser kedusha than something that is used in a shul in a manner not directly related to holy texts (tashmishei mitzva). Even if the yad is beautiful, it is an adornment of the mitzva of reading the Torah, not of the sefer Torah itself, as it is not designed to hang from or even touch the sefer Torah.
That being said, we should apply the balanced approach that poskim used in relation to non-kadosh religious objects. Neither tzitzit nor a tallit have kedusha.[14] Yet, the Mishna Berura[15] rules that although tzitzit may be brought into a bathroom, a tallit, which is used exclusively for the mitzva of davening, should not be brought there. It would seem that a yad, which relates to the sefer Torah and aids in the mitzva of its public reading, is no less deserving of dignity than a tallit, and a yad should therefore not be brought uncovered into a bathroom.
Nevertheless, if indeed your yad was never hung from the sefer Torah as an adornment, we propose that proper halachic balance requires limiting this stringency. The ruling against bringing a tallit into a bathroom is a recommendation, not a full-fledged halacha,[16] and the yad in question should not have a more stringent status than that of a tallit. One might also claim that it is not clear that a modern bathroom, with the hygienic conditions enabled by plumbing, is considered a “filthy place.”[17] Considering these two halachic factors, one could argue for leniency.
Still, we discourage you from taking the yad exposed into a bathroom. However, whereas a sefer Torah and tefillin may be brought into a bathroom only if covered with two covers, and at least one of these covers must not be the usually used cover,[18] significant opinions hold that one cover suffices for holy texts of lower level holiness.[19] In the case of your yad, then, we think that you may bring it into a bathroom if you keep it fully covered.