Do I think there might be some value in praying for the soul of your mother even though she was an agnostic and died without having followed a religious path? Yes, of course, and her appearance to you in a dream may well be an indication she needs your help.
According to my own Orthodox tradition, only those who have died in visible communion with the Church can be prayed for by name in public services, but this by no means prevents a person from naming non-Christians in his own personal prayers. Moreover, on the Monday after Pentecost, the last portion of the third kneeling prayer at Vespers contains intercessions not just for the faithful departed, and not just for those whose destinies are in doubt, but even for those whom we have reason to think may be damned:
Hear our prayer, and grant rest to the souls of Thy departed servants, our brothers and sisters in the faith, as well as to all our departed relatives and friends and others we wish to remember, for the authority over all things rests with Thee … The dead cannot praise Thee, O Lord, nor do those in Hell attempt to confess Thee, but we the living bless Thee and pray to Thee, offering supplications and sacrifices for the repose of their souls. For Thou art the repose of all souls and bodies, and we give glory to Thee, the Father, and the Son, and the Holy Spirit, now and ever and unto ages of ages. Amen.
You speak of Schuon’s chapter on “Universal Eschatology”, where he outlines five postmortem destinies: Paradise, Hell, Purgatory, the Limbo-Lotus, and Transmigration, and then you wonder out loud as to where your mother might be, though you add—and I would like to accentuate this point!—that it’s not up to you to judge. No indeed. And in any case do remember that Hell itself is not a finality, or not at least necessarily so. As Schuon points out, there is no symmetry between Heaven, which is “eternalized” as it were by its proximity to the Only Eternal One, and Hell, which the Bible describes as ai?nion, that is, perpetual and thus lasting only until the end of the ages.
You may be interested to know that it was the practice of Saint Silouan of the Holy Mountain to pray specifically, and with deliberate intention, for the souls of those in Hell. His disciple, the Elder Sophrony, recalls the following conversation between his master and another Athonite hermit. The hermit had said, “God will punish all the atheists. They will burn in everlasting fire.” Saint Silouan replied, “Tell me, supposing you went to Paradise, and there looked down and saw somebody burning in hell-fire, would you feel happy?” “It can’t be helped,” said the hermit. “It would be their fault.” The saint replied, with a sorrowful countenance, “Love could not bear that. We must pray for all.”
This conversation is mentioned in an essay you might like to read by His Grace Metropolitan Kallistos Ware. It’s called “Dare We Hope for the Salvation of All?”, and you can find it in a collection called The Inner Kingdom (St Vladimir’s Seminary Press, 2000).