If I have other coins, say 4 BTC, and want to spend 1.25 BTC, it's trivial to create a transaction with 4 BTC + 1 or more single-satoshi inputs, that pays 1.25 + 2.7500000x BTC change as outputs, and pay no fees.
So not only can they be spent, they can even be spent and pruned for free. Yes, I've done it myself.
First of all your trick only works once, if the 4 BTC come from a transaction output that is sufficiently aged. So it's not "free", you're consuming the limited resource (old coins in this case). You could not, for example, use the same 4 BTC again to combine another single satoshi input for "free".
Second, assuming that you did not have aged coins you would have to pay a fee. The 36 bytes for the additional input (the 1 satoshi) will drive the fee up by more than one satoshi. This is what we mean by "economically unviable to spend."