Wow, we're quite a bit off-topic here, aren't we?! The discussion is not about whether an archer can hit a 5' square from 100', the question is whether a silence spell cast on the arrow should survive the shot made. (Btw, longbows require a significant arc and really shouldn't be allowed in a typical low-ceiling dungeon, and a longbow would be best for attacking a square. A shortbow, such as the Turkish shortbow which the D&D shortbow is patterned after, would be hard-pressed to hit a 5' patch of ground and not skid another 40' or 50'.)
My ruling on silence cast on projectiles has always been that the arrow is simply being used as a spell delivery vehicle. If it hits a creature, the creature gets its normal chance to check for saving throws and spell resistance. If it doesn't hit a creature, but hits some other surface (which it must, eventually!), there is a 50-50 chance that the arrow breaks, disrupting the spell. If the arrow doesn't break, treat it as a grenade-like missile. When using a longbow (because sufficient height is available), the 5' square being targeted has AC 9: AC 10 -5 for Dex of 0 and +4 for shooting into melee (if applicable). Because targeting a square on the ground is more difficult that targeting an upright creature, I require a Spot check -- the square gains +2 circumstance bonus for each 5 points that you fail the Spot check. (No modifiers if you succeed on the Spot check.) Then, squares on the ground usually have at least partial concealment, even if you can see them, so there's a 20% miss chance. And it's 50% if you're just guessing at the location!
All of that means that the arrow is unlikely to hit the right square in the first place. And if it does, the spell may be disrupted anyway. This also takes care of the cast-it-on-a-tack-which-is-attached-to-the-arrow problem.
If a coin or other "unbreakable" object is used instead, all of the attack modifiers are still in place, but the range increment on throwing (10 feet) means you'd have to be right nearby to hit the targeted square.
One more thing. If they use a longbow outside and miss, use the grenade-like missile table to determine where the arrow did hit. If they use a shortbow or crossbow, use the same grenade-like missile scheme, but multiply the distance off-target (measured in multiples of 10 feet) by the range increment. This is basically what the RSRD says under "Throw Splash Weapon", but I've changed the multiple from 5 feet to 10 feet. (Come to think of it, I should probably change the direction from 1d8 into 2d4 to represent the fact that a bow shot from shortbows or crossbows will likely overshoot the target square rather than end up on either side or short of the target.)