Music students spend a lot of time studying musical notation, terminology, and theory. Of course, many musicians don't read music while they perform, so this emphasis on reading is obviously not related to one's ability to play their instrument. Rather, it's about learning the language that musicians use to communicate, and that is an important part of music education that we shouldn't neglect.
However, some beginners aren't able to read music, or they aren't able to learn to do so using traditional methods. It is therefore necessary to allow them to adapt, whether that means learning entirely by ear or approaching notation differently.
Sometimes, when a student is struggling to learn to read music, there isn't a problem that we can explain physiologically. There is no medical condition or learning disability to be diagnosed. As a result, the student doesn't require a special accommodation. Rather, they need to be taught to read music properly, using an approach that fits their learning style.
If a student can write letters or finger numbers over all of their notes, they clearly understand how the system works. The problem isn't that they can't read music. It's that they don't think about what they are reading in the right terms. They see notes, and they want to "translate" them to something they are more comfortable reading.
However, the problem with writing the translation in between the lines of music, besides the fact that too much writing clutters the page and makes it hard to read, is that you focus on the translation and never actually look at the music while you are playing it. You can't become comfortable reading something if you won't even look at it.
There are a few reasons that students might develop this translation habit:
Method books often print letters or finger numbers over notes when they are introduced. As students advance in the book and don't have these guides anymore, they start filling them in by hand.
Teachers present all of the notes at once instead of one at a time. Mnemonics like "Every Good Boy..." and "FACE" are all the student gets. Instead of continuing to study note reading until they are fluent, they memorize the mnemonic in a few minutes and forever after that rely on it to count lines and spaces rather than taking the time to learn to recognize a note immediately. Musical notation becomes a math problem when it should be a language, and stopping to solve the problem disrupts the flow of the music. Therefore, the student solves the problem in advance, so they can simply read the solution when it comes time to play the music.
Parents of younger students write in the translations for themselves to remind themselves when they are helping their child practice. The student sees this and assumes that's how things should be done.
The student simply isn't confident with their ability to read, and they translate because they are afraid they will forget what a note is if they don't.
Students need to be told up front not to translate their music. The moment it becomes an option, they are already caught in the trap. But in a case in which that didn't happen or the warning was ignored, the only thing that can be done is to start over. If the student is allowed to continue progressing, the notation will continue to get more complicated, and this will make the problem worse. They need to go back to the beginning and learn to read notes one at a time, sooner rather than later.