God absolutely does speak through thoughts, through the heart, and more.
God is "A" Spirit, who speaks by revelation.
Christ, who is God, lives in the born again...... and He reveals spiritual revelation to your born again spirit.
The words in the bible are SPIRIT and TRUTH.....so, that is not the same as a dictionary or an encyclopedia.
A Christian is taught the word by the Spirit of God, who is Christ in you, revealing it by revelation.
There is this word......"intuition"........this is a knowing that is not mental comprehension.....its an inner leading, that can be thought of as a "small still voice".
God speaks to your Spirit, is how you are led.
See, your spirit and God's spirit are in UNION, as "ONE With GOD, in Christ", so, this is not your mind, will, or emotions, this is your Spirit and your conscience.
When making a big decision, and you can't figure it out............. and you have this inner lack of peace........ or you have a complete peace........this is the Spirit, that is intuition, in action.
Here is an example.
Have you ever left the food store, after paying with money, and you get in your car, and you realize that the cashier gave you too much change back...... In other words, you under paid, because they gave you the wrong amount back.
So, your first REACTION, is......>"im tired, its hot, and i dont feel like going back in there".
See that? that is your SOUL REALM. = MIND.
But then, you discern a small still voice, a understanding that is your intuition, that is God's Spirit speaking, and it says...>>"go in there, and do the right thing".
See that?
That's God.