Barring individual performance differences between the two drives in question, there are no differences between an MSATA SSD installed in the mPCIe slot and a 2.5" SSD installed in the drive bay; they both consume the SATA III lane that was dedicated to their location.
My personal preference would be to use the mPCIe slot for a MSATA SSD to use as boot/system device so that I have the 2.5" bay for a large (typically non-SSD but perhaps bybrid) data drive...
As I am going to use the mSATA for a HTPC, it would seem that it would not require much storage space - a few programs and files. Would there be any problem with partitioning the drive as a boot drive and a home storage drive? Or, would you recommend using a smaller mSATA only for booting and use a 2.5 drive for storage? Thanks!
It's really a matter of personal preference and the way you plan to use it. You have to weigh the performance vs. cost question. I have more than one NUC and the usage for it largely determines the drive configuration. For example one is used for a Windows workstation. I have a 180GB mSATA in it with Windows installed. It works perfectly.
I also have a taller unit (supports both SATA and mSATA) that I use for an HTPC. That one has a small (60GB) mSATA drive with Windows installed, and a larger (320GB) SATA drive for data. I use the SATA drive to store movies, music, pictures, and recorded tv. It's just a cleaner way to set it up. Also, if the need ever arises I can just pull the SATA drive and attach it to another system.
There was a big cost benefit for me using the dual drive configuration. I was able to get a super-high-speed mSATA for relatively cheap because of it's small capacity, and a higher capacity "platter" SATA drive for storage for a good price as well. The storage drive doesn't need to be as fast because I'm not running my applications or OS from it. Combined I have 380GB of space with a total cost of less than $100 for the drives. I wouldn't be able to get under $100 for an mSATA that large.
Sorry for rambling on, but I hope this helps.
I am absolutely no expert on this issue, but for what it might be worth, I did read a review of an AsRock Beebox NUC that said it ran hotter with an SSD drive than with the just an mSATA. The reviewer though that there might be better ventilation through the NUC without the SSD.
Thank you for joining the Intel communities.
There is no difference on speed with this mSATA SSD or 2.5 SSD, neither with m.2 SSD; they can run at 6 GB/s, the information you all have shared with us is very valuable and very appreciated.