You would use Midi Out on your interface to your Juno Midi In, to send it notes/arpeggios/etc. You only need Midi Out on your Juno if you wanted to use it as a MIDI controller for softsynths.
Honestly most modern instruments use Midi over USB, so if you ever got newer analog synths in the future, you just need a USB port or hub. It's also possible to daisy chain together Midi cables, but I wouldn't even worry about it for now.
I'd probably go with the smaller Scarlett, especially if it doesn't need a power supply. I have a RME babyface (2 stock input channels powered via USB), and for a while I expanded it to 10 input channels via ADAT and I wasn't even using all those channels, so I sold the ADAT. I mean, my god, I can only play one synth at a time... I can't be a whole band at once. Its no big deal to unplug a synth and plug in a mic or whatever. Keep things simple.