To make the question narrower, let’s say how should I deal with a girl who has a very low self-esteem? We’re close friends and we may take this to the next level and form a relationship. IMO this is what we both want to. The problem is that she freaks out when message I her late. It seems that she thinks that I may consider her questions stupid or something.

What is the best way to soothe her and make a balance in our friendship/later, relationship?

Just reassure her that that isn’t the case.
Give her compliment her and make her feel special
I use to have really low self-esteem but it is a lot better now, thanks to my boy friend.
When we started to go out, I was so nervous that he didn’t actual like me, because I thought who would like me?
But he tells me every day that he loves me, and helps me through things I’m not good at, gently and with reassurance.
She just needs to know that she does mean something to you and you don’t think she is stupid
This may take a while, and it may be hard work at times, but her self-esteem with go up and she will become confident.