Holy crap, I never noticed that about the Shadow Temple's pedestal before!

The cross' inclusions are also questionable, considering how picky Nintendo can sometimes be about religious symbols in their games (though they are in the shape of an X, it's still hard not to see them as crosses).
They look like Saint Andrew's Crosses and with the way the chains are hanging from the ceiling and the blood is underneath, somebody or something was recently chained to them and tortured.

I haven't played this game in awhile, but doesn't the one in the bottom of the well have a hidden pit underneath that leads to an underground cavern with a pool of water that has skeletons sticking out of it - implying that once people were tortured on the cross, their bodies were dumped down the pit?

~ Kairobi King ~