Two cases:

• Your encoder is "smart" and is counting for you, so you only fetch the current value of the encoder, you are not counting the pulses.
• You are counting the pulses from your encoder and

First case

Fetch/publish the encoder value at any rate you need, or fetch the value only when you require it. Use time-stamps and everything should be ok.

Second case

You really shouldn't rely on "software" for this kind of task, you should set-up an interrupt on your micro-controller / microprocessor so that every-time a pulse appears from the encoder; a variable is changed to reflect the new encoder position.

The interrupt should do as least a possible so that you are sure every-time a pulse is triggered, your micro-controller is ready to enter the interrupt again. (don't do anything else than updating the value inside this interrupt, maybe just set the time-stamp of the data).

In an other thread, you should set up a loop that will get the current encoder position and publish it with a time-stamp. Make sure you don't have data races because the encoder position value is shared between the interrupt and the loop thread.