What are the long-term effect of riding with a chain that's too short?
The main problem with a chain that is too short, is when you're in a combination of gears where the chain is too short to go around both chainring and cog.
You'd have to be moving the chain from a lower to a higher-tooth count gear, so at some point in that first half-revolution, the chain will bind, the cranks will resist you, and any more force on the pedal will start to snap and bend components.
Since you've already ridden so far on the chain, it might be more a case of possibly a little short for optimal vs the catastrophic &quot;too short&quot; described above.  Or you've never ever put the chain into big-big.
Frankly I wouldn't worry, but when the new chain is fitted make it one link longer and see how that rides.    Remember to count links, not measured length when comparing it to the current chain.