The VT1 transistor is doing a level shifting/amplification of the input clock. The collector is using the ATMEG8 internal pull-up resistor which must be enabled for given port, PB0 in this case.
The internal pull-up resistor in the ATMEG8 ranges from 20k to 50K so it is a relative high value resistance. If there is too much stray capacitance on this line or the frequency of the clock is too high it can impact the waveform of the clock. I would probably opt for an external pull-up of a lower value to ensure waveform integrety.