Normall counter will not get multiple counts at low speed. The counter will not increment/decrement unless there is a state change in its triggering circuit. However, the total scan time (logic + I/O scan time) will limit how fast the signal may change without losing count. The minimum I/O scan time for T100MD+ is 2ms.
If you need more than 2 high speed counters, consider using two PLCs and they can communicate via RS485 to exchange data.