When people nowadays refer to the aron kodesh (the holy ark), they are generally speaking about the ark in the front of the shul, which houses the Torah scrolls. This ark is considered a tashmish kedusha, something that serves a holy object and thus is holy itself. Therefore, other items should not be stored in the ark. Additionally, even if an old ark is replaced by a newer one, the old one retains its holiness and should be treated accordingly.
The question arises: May we use the ark to store Chumashim, Siddurim, Haftarah scrolls (written on parchment), or Torah scrolls that have become unusable? It would seem that since all of these are of less holiness than a Torah scroll, such storage should be forbidden, as it would detract from the holiness of the ark.
However, a number of reasons have been adduced to permit this:
1. Since the Torah scroll is resting in the ark as well, the holiness of the ark is not diminished by these additional items. (If this explanation is correct, there is a problem when we remove all the Torah scrolls from the ark, as we do on Simchat Torah and (in some places) Hoshana Rabbah.)
2. The people who originally built the ark had in mind that it would be used for storing other holy objects besides Torah scrolls.
3. Since we customarily cover Torah scrolls with ornamental mantles, the ark is further removed from the scrolls’ holiness. It is now a tashmish de-tashmish, something that serves an item that itself serves a holy object. Therefore, placing other holy items in the ark does not detract from its holiness.
Notwithstanding the above three reasons, there are still those who insist that Torah scrolls alone, and nothing else, may be stored in the aron kodesh.