Can continuously changing polarity damage peltier module and more
importantly, will it be as efficient in reverse polarity?
Yes it can, I've burned a few out this way. You can kind of think of a peliter as a car, you need to slow it down or stop it before you go into reverse.
The problem is you've built up a thermal gradient when you pump current into the peltier, which in turn builds up a voltage gradient. If you throw the peltier into 'reverse' then there will be a large voltage gradient which can source a lot of current, when the circuit is reverse this can lead to a large amount of current being sourced until the thermal gradient across the peltier starts to reverse (a large thermal sink can take some time for everything to fully reverse).
This large amount of current has two effects:
- if the driving circuit is an h-bridge it can exceed the current rating for the mosfets (relays not so much but this leads to problem 2)
- the sudden change in thermal gradient can cause mechanical failures of the peliter
As far as efficiency goes, cooling will always be less efficient than heating because of the ohmic internal heating of the peliter. The material of each peliter also has resistance, this resistance causes heating related to the amount of current through the peliter (P=I^2*R). This internal heating means that heating something will always be more efficient than cooling it.
The cold and hot side markings (or in the datasheet) indicate whether it will cool or heat relative to the voltage placed on the terminals (kind of like polarity marks on a battery) as long as you keep track of the polarity, orientation does not matter for most applications.
What can be done about this?
If your using a control circuit (like a PID) a slew rate limiter can be used to protect very fast transitions. (I've ran this successfully in a number of designs and it protects against fully positive (or very high) on to fully negative, usually with 10's of seconds on the slew rate)
You can introduce some dead time logic to give some time for the switch from positive to negative.