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Programmatically all markers have a lifetime, such that they can be automatically removed. Is this the reason why markers also removed while on pause?

yes, most likely. rosbag is no magic, it essentially just replays message traffic it has recorded. (Interactive) Markers are also just messages, so if those messages are played back by rosbag and they contain a lifetime setting other than ros::Duration() they will disappear.

If yes, how is the right approach to solve this issue? Do I need to remove markers manually and not rely on lifetime?

Well. Technically if you pause rosbag play I would expect time to also 'freeze', so perhaps markers with a timeout should not disappear. But that will depend on whether you are asking rosbag to also publish the clock.

If they still disappear with --clock after you've paused playback, that would perhaps be a bug and should be reported.