No you will not have fan issues. Unlike the 27" model this system uses 2.5" laptop drives.
I've been messing around with a few of our newer 21.5" iMac's and I can tell you going with a dual SSD setup doesn't buy you much here. What I would focus on is upping the RAM. And if you go this far you might look at getting a larger blade SSD replacing your 128 module.
Besides going to a smaller SATA drive can also effect the systems performance depending on what you are doing here. Before you do anything make sure to make a full backup and go to the command line to break the Fusion drive set.
Last issue here is the newer 'Thin Series' iMac's are a bear to open and if you are not careful you can damage the LCD display. Get the correct tools and follow the IFIXIT guide to the letter as it doesn't take much here to kill the display (black bars).