How do you disable tracker crawling?
Why would you do that? That breaks gallery and media player.
The issue is with tracker out of the way, there will be no proper metadata from the images, no favorites functionality as well. The pictures not showing up is a side effect of tracker not indexing them. I am not entirely sure how can I detect deletion of pictures without tracker. An alternative approach would be inotify but I am not yet sure if it can be done without breaking usb mass storage mode...
Cameraplus uses names like: 20130820_001.jpg, 002, 003, ... etc If you remove 003.jpg then the name will be reused. I did a change to camera+ to let it keep track of the last used counter value and thus will use 004 in the above case instead of 003. That should at least prevent the wrong timestamp in the file but not really fix the problem...