Encrypted partial backup in Dropbox I'm storing the majority of my documents in Dropbox. 
I store all my passwords in 1Password (with encrypted backup in Dropbox).

I also have a large pool of files (SSH keys, SSL certs, encryption keys) that are spread across several folders. Is there any software, that would allow me to easily copy the content of these folders (with subfolders) to Dropbox in encrypted form?
I am not so much familiar with Dropbox, but I'd assume an encrypted sparsebundle image would be suited quite well fro your task. For instance this site explains the procedure. 

In essence you have to: 


Open Disk Utility
Click File > New > Blank Disk Image...

Customize your encrypted image file. I'd suggest to use sparsebundle disk image since it consists of smaller files and will probably result in better syncing performance with Dropbox.
Choose a strong password (and optionally save it in your keychain)
Now you can double-click the image file and it will open as a volume.


This is very safe and efficient. I even use a sparsebundle image for my TimeMachine backups.