Sounds like your at the crossroads as many of us are with the home server. At this crossroad we have choices on hardware and the OS.
[Hardware considerations] The EX490/5 hardware wise is showing it age and has been discontinued by HP, so replacement parts are going to be used.
I do not believe the server hardware caused your hard drive failures per say, any more then any other hardware could cause a drive to fail. Heat, these servers are densely packed on the drives and are designed to filter dust/lint/dirt which could case heat (if not kept serviced) which could cause hard drive failure because of that heat. All hard drives will fail at some point, price can effect how soon they will fail but not solely, heat and the environment can effect the life as well.
Using these servers you don't have an option for hardware raid for the OS.
So using these servers going forward is going to be a personal choice, you are going to want to invest in spare parts if you do and you are going to have to understand that you don't have raid for the OS.
Also, as far as having drives inside the server or out in the external. You need to think about that connection. I have seen problems with drive access from external drives and that is a whole other topic, bottom line I would try to keep the main drives in the server and use the external for backups as the backups can handle intermittent connections better then the main drives.
[OS considerations] You have chosen 2012E and by making that choice you have lost DE and all the recover-ability that came with it, so now we need to think about how we will setup to regain that back, because at the end of the day it's all about the data and uptime and when something fails how easy and fast can we get that system back up.
I hope this helps and not confused you more.
What I do on servers and PC's is focus on protecting the data, I don't worry about protecting the OS. For me, I don't install a lot of stuff on the OS so it is disposable to me. I am willing to rebuild the OS when needed and not worry about raiding it. I focus on keeping the data backed up.
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