Heat issues

Get the iStat Pro widget and you will be able to monitor your temps. My late 2012 mini gets warm on top when I am using handbrake or compiling some code. Make sure there is nothing around the bottom of the mini and that there is nothing on top of it. The mini pulls air in from the bottom for cooling and the aluminum case helps disperse heat.

http://istat-pro.en.softonic.com/mac

The heat is coming from the CPU/GPU and heat sink attached to them. The second drive in fusion can create a little heat but it is very minimal. The SSD and HDD in my fusion are always around 30-32C while the CPU hits 100C so it is unlikely the heat you feel is the drives in the Fusion. Lag could be low RAM or the discrete GPU if you are talking about games. You didn't say what Mac mini and RAM you have. Also more RAM increases the RAM available for the GPU.

As noted, iStat Menus gives you all the details you need. It's a great app if you are heat conscious - although it has been known to drive paranoia as well

When I had a mini with twin disks (HDD + SSD) yes it did get to work harder. That's more because the file system can shove more data to the CPU/RAM system.

I used to play skyrim on mine and internal temps approaching 90 were common but still within the safety envelope.

As long as the mini is well ventilated (I mean not covered or blocked in too much), it should be fine.

its a nice little toaster when working.

Something like iStat menus will show this, but the system will shut down if temps get too high.