This is the DMs call, in most cases there is no difference
It is well established that the D&D rules do not adhere to the rules of physics, just look at falling damage. D&D is not a physics simulation, it values speed of resolution and simplicity of rules far over accurate modeling of physics. The reason for this is that for most players it is no fun to break out the calculators and compute acceleration or solve trigonometry problems in the midst of a heroic fantasy session.
For cases where this would lead to egregious deviations from expected outcomes and break immersion of the game's fiction, the game relies on the DM and common sense to make ad-hoc adjustments and rulings as needed. For example if you could turn an arrow into water in mid-flight, this might call for such an adjustment.
However, look that the materials that Minor Alchemy offers:
You perform a special alchemical procedure on one object composed entirely of wood, stone (but not a gemstone), iron, copper, or silver, transforming it into a different one of those materials.
So your arrow will consist of wood, stone, iron, copper or silver. They are all hard solids, and their flight behaviour will be quite similar. The simplest way to deal with this is to rule that it has no effect, unless you are trying to hit a werewolf and you just lost your silver projectile.
Why only "in most cases"?
There might be special situations where it is worthwhile to get into the details, for example if you come up with an elaborate plan between sessions and can clear this with the DM without wasting everyone's time. At most you can create an object of 5 cubic feet because the feature also says
For each 10 minutes you spend performing the procedure, you can transform up to 1 cubic foot of material. After 1 hour, (...), the material reverts to its original substance.
Let's say you obtained and want to abuse a trebuchet. The DMG (p. 256) says it is typcially throwing a Trebuchet Stone for 8d10 bludgeoning damage. Trebuchts came in all forms and sizes, but a typical medieval one apparently threw stones of about 100-200 lbs, so lets assume it can throw that.
If you look at the specific weights below, that would allow you to throw a wood ball of all five cubic feet in light wood. You could turn an iron ball weighing close to 3,000 pounds into this wood (worth 300 gp; a copper ball would cost you 1,500 gp in material, and silver, 15,000 gp but would be even a bit heavier ... which is unlikely to be needed, read on).
If you let it revert at the top of its arc, timed everything just right and calculated correctly how much slower it would progress from there to pinpoint where it will drop, it could deal considerable falling damage from a height of 200 feet. Possibly 1500d6 bludgeoning using the assumption it linearily multiplies the damage it deals for dropping 10 feet.
That amount might be worthwhile going through the motions. Of course, it would depend on your DM playing along. They might just say nope, it's 15 times the heaviest stone, so it will be 120d10, or, they might say, nope, we'll use the CR 17-20 deadly trap (DMG p. 121), and the cap is 24d10.