The reason two cells worked in your scale is that the scale is internally regulated to compensate for voltage drop as the battery runs down. If the scale worked with two of the 2025 cells, there's no reason to expect it'll suddenly stop working or sustain damage -- if that were going to happen, it would have happened either immediately on inserting the cells, or as soon as the device powered up.
That said, a spacer (for the dimensions you give, a US or Canadian five cent coin might work) on the flat end of the cell is preferred over a second cell. If you're trying to substitute a thinner cell in a device that hasn't previously been tested, this will ensure you get the correct voltage and avoid the risk of damaging the device.
Worth noting that using 6V instead of 3V with cells this size poses no hazard other than possible damage to the device. There isn't enough current available from this type of cell to start a fire (short of a device specifically designed to do so) or produce a shock you can even feel (except on your tongue, or again with a device specifically designed to step up the voltage). With much larger cells (say, the size of those that make up a car battery or radio control model power pack), there's a slight possibility of fire or burns, but even then, 6V won't give a shock you can feel on dry skin (likely not on damp skin, either).