The internal pullup resistors might be considerably higher in value than 10k - perhaps 50k. (I don't have the Attiny45 datasheet handy, but another AVR datasheet lists 20k to 50k for the Atmega328). That might be too high for this application; without the datasheet for the encoder I can't say.
The external 10k resistor will allow faster rise times on those input signals, or cope with the capacitance of longer cables, or allow better logic levels if the encoder has significant "off state" leakage current.
It makes sense to design the schematic and PCB to allow fitting the external resistors (unless size or weight are REALLY critical for your application - you can always leave them off where (perhaps the cables are short) you don't need them.
EDIT : the encoder datasheet tells you precisely nothing useful in this respect. However, IF this sensor is representative, (links to this datasheet) the "output leakage current" is maximum 10 microamps : with a 50 kilohm pullup, that means an output voltage 0.5V less than you expect. I'd probably play it safe and add the resistors : 10k would be fine.