I don't know if there's a limit to the number of bookmarks you can have, but if they are that important and there are that many then I would suggest a more permanent solution.
You could create a new layer and whenever you need to add a 'bookmark' just use the shape digitizing toolbar to add a rectangular feature (easiest would be the 'Add rectange from Extent') the same size as your current canvas extent.
The advantages of this are that the 'bookmarks' are saved off permanently as data, you can add notes and type fields so you can filter them, and they can be used later in an Atlas if necessary.
EDIT: Step-by-step instructions
Enable the Shape Digitizing Toolbar in 'View' > 'Toolbars' > 'Shape Digitizing Toolbar'
Create a new layer:
- 'Layer' > 'Create Layer' > 'New Shapefile Layer' (I'm personally not a fan of this format but it's good for starting off)
- Choose a location and name for the shapefile, set the geometry type to polygon
- Add any fields (columns in the attribute table) that you would like (you can also add these later)
- Click OK
Add a feature:
- Select the new layer in the Table Of Contents on the left
- Enable Editing by clicking the yellow pencil icon (you should see some editing buttons turn from grey to coloured)
- On the Shape Digitizing Toolbar click the drop down arrow to the right of the rectangle and choose Add Rectangle From Extent
- Click once in the top left of the current map view and once in the bottom right to draw the rectangle, right click to finish, add any attributes you want (if you added fields).
- After you've added the features you want click the Save Edits icon (different to the save project icon!) next to the pencil and then click the pencil to stop editing.