A couple of points:
- The audio interface has no effect at all on the internal sound processing Sonar or any of your softsynths do. The only place where sound quality of softsynths comes into play is the DA conversion. It is doubtful you'd be able to hear the difference between the various mentioned medium and upmarket devices, although really cheap devices can sound flat and lifeless.
- Latency is where the audio interface and its drivers come into play. While Thunderbolt can in theory do better than USB, really the drivers make a huge difference. E.g. my RME UCX gets 2.9ms roundtrip at the lowest buffer setting and even their own new Thunderbolt enabled interface the UFX+ shows that USB is no slower than Thunderbolt. It's the track count that's the bottleneck. If you don't record a huge amount of tracks at the same time there really is no reason to go for Thunderbolt specifically.
- Latency will always be affected by certain plugins, independent of which audio interface you use. E.g. limiters with a look ahead function, pitch correction plugins, convolution reverbs and linear phase EQs all induce significant amount of latency simply because of the way they work, you can't really change that. When such a plugin is inserted on one track, Sonar will delay all the other tracks by the same amount in order to line up everything correctly on playback. During recording, you can get around this by hitting the PDC (Plugin Delay Compensation) button, which disables this artificial delay for the track you're actively monitoring. This only works if you don't have any of those delay-inducing plugins on the signal chain of that track, of course. Again, this has nothing to do with the quality of the interface, it is necessitated by the process.
EDIT: good point about Nectar having a tracking/mixing switch. Some plugins do. Linear phase EQs usually have a non linear mode too, and Waves makes a "live" version of their convolution reverb IR1 if you want to use it during tracking. /EDIT
I would also concur with hbarton that it would be a good idea to talk with a store representative to see if you can get an easier way to hook up a bunch of synths without needing a million inputs on your interface. You can only spend your money once and it seems like a waste. Traditionally, what you're describing is solved by having a patch bay - as an example, you would have all of your synths plugged into the backside of a patchbay, say on the top row. Then you hook up your interface inputs to the backside of the patchbay as well, but on the bottom row. Now you can use short patch cables to quickly patch any synth to any input on your interface, all from your comfortable desk chair.