What's your budget? And what are you doing with this box? "Terminal server" defines how you interact with the machine, not what it does. Will it be running services? Loghost? Email? Apache? SQL?
To answer your question, as far as I'm aware embedded devices share the PCI(e) bus, so there's no significant difference. Choice of chipset is going to have a much bigger impact than onboard vs add-on. Depending on the application(s) other factors may end up being a bigger indicator of performance. If you expect to have a lot of users, I'd focus on maxing disk I/O rates long before worrying about the network cards.
But seriously, fuck that shit. Just order a Dell Poweredge and be done with it. They're quite reasonably priced for what you get, but if you're strapped you can get a used one a year or two out for a good price and still have it be quite powerful.
Also, I would not use a solid state drive in any application where reliability is a concern, especially without redundancy in place. If you're expecting a lot of activity the drive will wear out quick and you'll end up with a fancy paperweight for your desk.
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I wake up in the morning more tired than before I slept
I get through cryin' and I'm sadder than before I wept
I get through thinkin' now, and the thoughts have left my head
I get through speakin' and I can't remember, not a word that I said
- Ben Harper, Show Me A Little Shame
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