The season 5 will be in 3D?

no it wont it was just a trailer in 3D but it wont be it will be in 2D i mean in the original

yes it will look in this video

I think somewhere I heard that it will only be 3D when the Winx are underwater.

Well, according to the creator, it will. There is multiple errors-
Stormy's stockings
The Trix's gloves
Transformations- In 3 13, if you look when Bloom screams after Tecna ''dies'' if you see closely that she has the Enchantix.
They're doing it for the errors and because they'll be in another dimension- they did become guardian fairies and graduated from Alfea already.