If you use MarsEdit and its media manager is showing hardly any of your photos, the problem is most likely your setting in the Photos app for iCloud Photos.
You have two choices: “Download Originals to this Mac” or “Optimise Mac Storage”.
If you have it set to download originals, all your pictures will show up. If you have it set to optimise Mac storage, you’ll just see a random smattering of images.
While troubleshooting this with Daniel Jalkut, the author of MarsEdit, he mentioned he was looking at ways to address this including, perhaps, using a newer Apple facility to access the Photos database. As SSD space on Macs remains limited and image resolution on iPhones expands, I hope Apple will make it easier for developers to deliver what users expect.