No, what you did to transform them still happens. Think of them like trap cards but in minion form.
For example: mind-cage oni.
When your honest casts a spell, he transforms. Its ability says “when your opponent casts a spell, put a copy of that spell into your action bar.” So, your oni will reveal itself, put a copy of the spell that transformed it into your action bar, and then the opponent’s spell will resolve.
The reason this can be broken is because chromatic cold, for example, will dispell the oni before it’s effect, meaning you don’t get a copy of the card.