No you would not have seen the System Reserved partition when booted from that drive. but when under another OS you will.
There is no effect from having the partition there other than it taking up space.
If i was you and didnt want to have the RAID 1 anymore i would re-format / partition the drive you cannot see any data on. then copy the data from the working drive to the freshly formatted data drive.
then you can format working drive and you have 2 fresh drives 1 with all ur data on it.