Beautiful game worth the wait. Having played through, in one frenzied sitting, I eagerly await DLC and more content. Anyways.
List of secrets i've found:
1 - At the extreme leftmost part of the map, the upper dead end, kneel on the top step for a few seconds to gain 200 relics.
2 - In Arezon Cathedral, in the Library subdungeon. On the first floor, instead of riding the elevator up to the second floor, jump off it to reach a secret room with the SiNiSistar 1 Otherworlder Eye staring at you in the background. Interact with the prompt to gain an item (Sacramento) that increases relic gain.
3 - At the bottom of the valley, move right from the statue of the Goddess to the next room. Use the Scivias Powder to reveal a slug. Kill it to gain 500 relics. (Or don't, it's a lil cutie that can't kill you~)
4 - On the road to the Demi-Human's cave from the upper-left most statue, proceed onwards to the area with two pillars that does not contain any enemies. Use the Scivias Powder to trigger a secret Boss fight with Seere, an Otherworlder. The reward is the best wand in the game. (This is the entry in the gallery that asks to use a particular item under the Highway category.)
5 - Not really a secret, but keep an eye out for the after-credits scene. A nice callback to SiNiSistar 1, and a stinger for future content?
I'm not sure about others, please ping me if there are any that i've missed!