Tokonoma have no religious significance. They simply indicate and serve as decoration for the kamiza - the seat of honor in a house.
All that said, there's a danger in taking things too far. Some people ascribe more meaning and intent to Japanese courtesy (and terminology) than even the Japanese
I've said this elsewhere so I'll repeat it briefly here again, since, apart from those with military experience the formalities of address and deference are very slim in Western society -- but they are not entirely lost in concpet or fact.
This recurrent debate touches on knowledge about Western traditions in distinction in forms of respect versus worship, which in the West is matter of some significant thought. .
Dulia is a Greek word in theology that is distinguished from "latria." "Latria" is "worship" given only to God. "Dulia," on the other hand, is appropriate to any human being, alive or dead (typically dead), or even worthy inanimate objects. In Classical Latin the term used for both was "servitus." Early Christians failing to render "servitus" to the emperor, for example, were the similarly the cause of much controversy, which may have been as much linguistic as it was political, not unlike the debate about Japanese forms of rendering respect. While that usage elided the distinction made by dulia/latria in Greek, Orthodox theology held the two are different in kind and not in degree, as early as St. Augustine, as they remain.
The most closely related words in English to "dulia" are veneration or homage.
Dulia or homage can properly to political superiors, objects of great beauty and reverence, or people of superior quality, living or dead, without verging into worship. All of these are typical of Japanese observances toward kami of various types (including, ironically enough, the Emperor.)
What is done in the dojo toward the tokonoma is homage due and paid and nothing more.