I don't think it will limit the life of the heater to run water through it all the time. To the contrary, stopping the flow of water through the heater would probably shorten the life of the heater more if you take into account that there is salt in the water and letting the heater dry up would certainly create some corrosion. Having a bypass would be effective if you ever had to do repairs on the heater, but you could certainly create a bypass when and if that happens. I don't have a bypass for my heater and run the heater pretty infrequently.
The advantage to having a bypass is that your system will run more efficiently when the heater is bypassed. The disadvantage is that a bypass means more parts, which means more ways for things to fail and more ways to make mistakes. For example, certain incorrect settings on a bypass can damage the heater (i.e. turning the heater on with one side on and the other off).