In theory the shorter port would have a smaller air mass than the longer port, therebye offering less resistance and being tuned higher. This shorter port would be unloading at the lower frequencies that the longer port would be tuned for, rendering the long port's tuning range useless. If the longer port was substantially longer, it might have enough air mass that it would not effect the shorter ports tuning range, acting as if the longer port were alltogether not present, so the short port could do its job at the higher tunning. But this is unlikely the case, and pointless if executed.
In the case that the length of the two ports is very similar, the overall tuning of the system will take on the characteristics of the shorter port, but when playing frequencies below the shorter ports tuning range, the short port will unload first and more easily than the long one, and therefore generate more port noise, wind, ect than the longer one would.
The only time port lengths should differ is when port diameter differ also e.g. mixing a 3" and 4" diameter port.