I don't know about third-party software (which you must hope continues to be supported), but you can create encrypted disk images in the OS:
When chooseing the image format, I would suggest Sparse Bundle Disk Image as that can be efficiently backed up by Time Machine.
Take note of step 10. You probably do not want to store the password in the keychain.
A disk Image mounts just like a hard drive. When you eject it, the file is encrypted again.