Is it recommended to upgrade runes below Ort?

It depends, are you playing on the ladder?

There are a few ladder only rune words, such as Spirit that uses common runes (Spirit is TalThulOrtAmn).

In those cases, it helps to keep those lower runes without cubing them.

Also, there are recipes that allow crafting that uses specific runes, and good crafted rings/amulets are in high demand.

Finally, you can cube Ort into higher runes, at that point you just need to find the proper gem to go with it. This was put in as of patch 1.10.

With enough runes and gems, you can now cube El runes into Zod if you wish.

The lowest level of runes I'd actually start keeping is Ist (Ists are always useful due to its magic find bonus)