I do not use Aegis anymore, I use KeePassDX instead. It works for TOTP just fine.
JuiceSSH is still under development?
Some people don't like to keep passwords and TOTP in the same place.
Why? Both are on my phone, although KeePassDX database is exported and backed up. I do not use the desktop application, but I might.
If it is compromised, both your passwords and TOTP are compromised, which kind of negates the point of multiple factor authentication. If they are in separate apps, hopefully both won't be compromised, at least not at the same time.