Here's one tally of the shuttles destroyed, damaged or otherwise misplaced:
http://www.ex-astris-scientia.org/inconsistencies/inconsistencies-voy.htm
The structure of the
Voyager, with Main Engineering far aft, seems to severely limit the size of the main shuttlebay. OTOH, the interior sets were built to feature corners and dividing walls that conveniently make the sets very small and affordable while suggesting a larger, multisectioned overall facility. The combination makes it very difficult to believe that there would be lots of space onboard for storing entire shuttlecraft - but the maze also allows for fun things like the "Shuttlebay 2" often mentioned in dialogue, or the putative shuttlecraft construction workshop (which may in fact have been the same facility we saw in action constructing the first Delta Flyer).
Kirk's ship supposedly had four shuttles of size similar to those of the
Voyager (or at least "all four" is how the shuttle complement of sister ship
Exeter was described). There may also have been other types of shuttle aboard, such as the special variants we saw in TAS - but TAS also suggested that those variants were crowding the upper hangar deck, which in TOS was always empty, so the TAS contingent may have been temporary, for the duration of specific missions only.
Janeway's ship is roughly the same size as Kirk's, in terms of the shuttlebay area at least. It thus wouldn't seem likely for Janeway to have more than half a dozen shuttles aboard initially - perhaps an even mix of the Types 6, 8 and 12 often seen, plus possibly one example of the unseen Type 9 mentioned in "Resolutions". All those types were said or shown to be warp-capable at one point or another, and there were certainly more than two examples of each of the types (save the unseen 9) in evidence - at least two of each were destroyed or probably destroyed. So it would indeed seem that our heroes can build new warp drives for new shuttles, although perhaps only out of an existing stock of spares.
It doesn't really sound all that illogical. Surely this 24th century starship should be a veritable high tech factory, and surely it could churn out things like shuttlecraft, provided it had properly functioning replicators, and got the necessary raw materials from friendly ports. For a total of 17-18 lost (and perhaps the same number constructed), we get an average construction rate of less than three per year, which doesn't sound like much.
Timo Saloniemi