But if the fuel is something that leaks out from the pipes in gaseous form, then it quite plausibly follows that some of it will remain in the tanks in unusable, inaccessible quantities (just like it's impossible to actually empty
a bottle of nitrogen through a valve - at best, you can bring it to atmospheric pressure). Until the shuttle reaches vacuum, that is.
Most of the modern spacecraft have a special system for driving out the last drops or whiffs of fuel/propellant (a separate purging gas, a piston or diaphragm, whatever). Starfleet engineers might not bother with such pennywise things.
SULU: Steady. No, Mister Scott, bearing three ten mark thirty five just cleared. No antimatter residue.
SCOTT: All scanners, spherical sweep. Range, maximum. They'll have to pick it up.
UHURA: If the shuttlecraft powered away, Mister Scott, but if it were just towed?
SCOTT: There'd still be traces of residual matter floating around, Lieutenant.
This is intriguing. Why isn't
there residual matter floating around?
I mean, the shuttle was
towed away, as far as we can tell. The shuttle also arrived at these coordinates under its own power. If it is natural for a shuttle to create an antimatter residue trail when traveling under power, then there should be residue in evidence right there, and not merely at "bearing 210.40".
It almost seems we are supposed to think that antimatter residue is only associated with calamities, not with normal operations. That is, there would be residue there if the shuttle met an immediate grisly fate, or fell prey to a conventional attack and either limped away under power or was towed away - but not if it just sailed on. Scotty would still have to do the residue scan under this scenario, because an undamaged shuttle traveling under power but failing to transmit anything would be impossible to locate - Scotty's only "hope" lies in searching for a damaged craft.
ranging from the warp engine, hyperdrive and ion engine
None of the dialogue necessitates these being different things, though. The shuttles just get their FTL engine power from ions ("ion engine power"), while the ships get it from antimatter. It would require pretty explicit dialogue to drive a wedge between "conventional" warp drives and the drive that moves the shuttles at FTL, seeing how both rely on obvious warp nacelles, later in TNG era graphics seen housing obvious warp coils.
In my personal perverseverse, this "ion engine power" thing ties directly not just to the "ion propulsion" of the Eymorg but also to the "polaric ion" thing from VOY, and to the "cascade ion drive" from Dave Stern's ENT novels. But it also relates to antimatter: it's just that these polaric ion cascades are an alternate means of regulating annihilation, a method (unsuccessfully) competing with dilithium. If the regulation fails (as it often does in large scale applications), it's kaboom time, for obvious reasons.
A related idea would be that in the conversion of annihilation energies, dilithium is a brute "shortcut" such as those used in getting electricity out of a chemical battery today, but the polaric ion cascade is akin to the electron cascades used by nature in getting electricity out of a chemical battery - more gently and more efficiently. It's just that brute systems can be overengineered to cope with overloads; the gentle cascade is intolerant of excess.