It might of course be that warp drives are expensive but surprisingly modular - and one can be installed inside the nacelles of a shuttle in a matter of hours, or taken away, and most shuttles make do without it.
Shuttles that were explicitly said not to have warp:
-Type 15 pod in "Time Squared"
-Type 7 shuttle in "Q Who?" (but we later saw that one doing interstellar journeys)
-Type 10 shuttle in "The Sound of Her Voice" (but we supposedly saw that one doing an interstellar journey in the dream sequence of "The Search")
It might be best to just invent excuses for why each of the statements was in fact a special case and each type in fact is capable of warp "normally".