Speaking as a step-parent.. I wouldn't try to interfere with decisions that are made regarding the child, however I WOULD always expect to be kept abreast of anything that is going on.
My DSS lives with us, so I admit that this probably makes things slightly different. But, my partner works full time, so when he gets home from school, it's me he sees. It's me who helps with his homework, and it's me who chats to him to see what's been going on, and if he's had a nice day.
This means that if anything is going on, I need to know about it, as I need to be completely on the ball and able to react to things and make decisions based on what I know.
If he was going through anything, I would absolutely expect to be told - because he spends so much time with us (and often alone with me) that how could I possibly care for him properly otherwise?
As much as you might not like it, your ex has been with his partner for 9 years, which is a long relationship. It means that this lady has been in your child's life for a long time now, and whether you like it or not, she isn't just going to sit there and ignore your son at home - of course she's going to be involved. Do you want her to let him make his own meals? Wash his own clothes? Take himself to school? I'm not say she definitely does these exact things, but there will be things that she does for your son when he's with them that you would do for him when he's with you.
That is the reality of the situation, it is what it is.
Your son could easily have ended up with a step mum who doesn't give two hoots about what he gets up to or how he is, but as you said yourself, this lady is nice, obviously cares for your son, and wants to be involved. Whether you like it or not, she is involved, and lives with your son just as much as you do.
You need to work together on this, she lives with your son, of course she is going to be involved.