RME Babyface Pro vs. Apollo Twin USB DUO

USB is not Thunderbolt, quite different technologies though the latest Macs use the same socket for both.

Don't know why anyone would say Thunderbolt has "zero latency" because nothing can. It takes time to convert audio to digital and vice versa and no way round that.

For audio purposes USB3.1's bandwidth is irrelevant, as is Thunderbolt's. It's unlikely an interface can shift enough data to max out USB2. I use an RME UFX connected to a Thunderbolt to Firewire adaptor on my MacBook Pro and it easily handles everything the UFX's 12 inputs can send to it at 44.1KHz, including monitoring most inputs via Logic. If I don't mind a round-trip latency of around 12ms I can add another 8 inputs via ADAT, and still Firewire handles it OK.

Data throughput higher than USB2 can handle is maybe an issue if you need the number of inputs and outputs a big studio might need, but for most purposes it's fine.

As for latency, I can get a stable under 3ms round trip using USB2, USB3 or Firewire to Thunderbolt so long as I don't load the DAW with plugins much and don't try to monitor more than a few channels through the DAW. I usually track and sequence at around 6ms round trip latency which in the real world is fine. Unless you have diffculty keeping in time with an amp or drummer six feet from you because it takes 6ms for their sounds to reqch your ears.

Apollo vs RME I have no opinion on, only having used RME. What I can say is that historically RME have been very good at supporting discontinued versions of their products rather than putting you in the "new version of the OS is out, so here's your chance to shell out loads of money on our latest product - or stick with one we no longer offer any support for at all" loop.

And never assume your input/output needs of today will be the same in a couple of year's time.