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Looking at the Rogue Trader book, they offer nothing smaller than Star Destroyer sized vessels. With Frigates being the smallest warp vessel listed, are there others that are smaller? Do they have exist in any numbers? Are frigates simply shown as the smallest due to that being the most minor a Rogue Trader would bother with?

Is this potentially a hold over from Gothic where that is just the smallest size mentioned? I am aware that there are other smaller vessels, but it sounds like they are meant for in system travel and not interstellar.

Certainly not in any numbers.
The smallest warp-capable vessel in use in any numbers is the Viper-class - and it's still nearly a kilometre long!

http://warhammer40k.wikia.com/wiki/Viper-class_Scout_Sloop

There are odd archeotech examples of small gunships and vessels being warp-capable, but this is the sort of thing that's only in the hands of the Officio Assassinorium or the Inquisition. certainly nothing a 'normal' citizen of the imperium - even a 'normal' starship captain - would even be aware existed, much less actually encounter.

There are smaller ships which aren't warp-capable, but obviously these are of limited use to most people.

Thank you, this is exactly what I was looking for. So the Viper is noted as being the absolute smallest standard Imperial vessel.

Thank you!