No problem at all, from what I can understand.
As long as you use valid pens, markers that are intended for use on CDs etc. I remember when I decided to copy back over 2000 dvds and throw them away as I moved over to hard drive storage. It took forever and of all the discs only six or seven of them gave me read problems. Some files where damage, but the reason for that was .avi files and burned with XA Mode 2 that I used for video files. So less error detection and error correction. And I always had good quality media, and always used pioneer burners, first one was 4x I think.
Anyway, I had written on them, and the movie discs had even more text on them, all stored in cakebox, away from sunlight and in room temperature. Even the CDr discs burned on a Plasmon 2x writer from the 90s I could read without any problem some where gold discs others where not. Even some cheap crappy media was fine to. All my discs had writing on them with proper pens, so I can guarantee you will have NO problems as all.
When storing in cake box, remember the disc at the bottom can scratch, I used the tiny plastic ring that came in most of the cake box at the bottom to lift the stack a bit so if you move the boxes around that disc will not scratch, or you can use a coaster disc at the bottom.