Yes, for several reasons.
(1) Your military flying has validity to any civil flying you do, but the reverse is not true. So having a common record of military + civil is useful.
(2) Military time flights from take-off to landing, civil world times flights from brakes-off to brakes-on. So, the flight times for your military and civil records are different. (okay, more relevant to a fixed than rotary pilots).
(3) It's just plain nice to have a record of all of your flying in one place.
It's worth doing a bit of shopping around to find the logbook that does this best, no logbook is genuinely expensive, and it's worth finding the one that does the job for you best.
G