The bookmarks are kept on the server.. It has to transfer them to you, and it has to store them. 200 bookmarks for 1.3 odd million customers.. works out to be a lot of bytes.
Considering they keep track of every single thing you've scanned/discovered, and what level you've scanned it at, and whether you have sold the data or not, I doubt this is the issue.
(You can go back to a system you only partially scanned and then sold the first time, and scan and then sell the remaining bodies; I'm not sure if you can L3 something you only previously L2ed or not, they may not store the level once its sold, but they definitely keep track of discovered vs detail scanned.).
I would love to see folders/categories/colors/filters for bookmarks. If its a performance issue, the filters/categories could limit how many bookmarks are being displayed. They could also have "global" bookmarks that are always visible (and limit the number of those), and "local" bookmarks that are only shown if I am currently within a 1000ly (or some number) of them.