Ok to answer all your questions.
can he ask a question here even though he's not 13
If your son is under the age of 13, then you must supervise him while he is on the website, and give him permission to use the website. Because the administrators cant go looking through every single thing that is posted here, we cannot guarantee that the content on the website is safe for users under 13. We cannot be responsible if your child sees objectionable content on this website. Once you understand these things, he may make an account under your supervision.
do you have to pay to be a member
No, BVEStation is free for anybody who wishes to become a member.
i didn't ask permission before downloading is that only for modifications only
You are free to download any file listed on the BVEStation downloads page, and use them with BVE2/4/OpenBVE. Permission is only needed if you plan to or want to modify the downloads in anyway, or if you want to redistribute the files. Redistribution for private use is allowed, as in within your home, on multiple computers.
can my son ask a question about bve4 in my account as he is under 13
I just answered that, but if you want him to use your account, you may.
download the whole index site a once the what does this mean
This means you cant go on the BVEStation Downloads and download every single download on it at once. I highly doubt you would know how to do that anyway.
i just logged in and i only have one account but my username works with my email and my user name too
Thats normal.
I hope I answered all your questions, and if you have anymore feel free to ask.