If they are not separated you should try to keep both of the same type and condition. Although, if they are only paralleled during active charging and are disconnected when the charging system is not running it would less of an issue.
I think over time you'll probably see one battery age quicker than the other. If I had to guess I think you'll ruin the deep cycle faster than the starter in this scenario, unless there's some sort of current limiting on it when they are brought into parallel. Deep cycles do not like a high current, short duration load and the in-rush of a depleted starting battery would want all the current it can get. In this case the second battery would react much faster than the alternator to fill it, thus the need for a current limit.
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