IoT HAT is more affordable
Only $9 you get both Wifi and Bluetooth functions for the price of one dongle. And if you are using Pi Zero, you may also need to purchase USB OTG Cable and USB Hub with Power Adapter. Ut is advisable to have independent power source for your Wi-Fi and/or USB Bluetooth dongle(s).
The setup is more orderly
Because you do not need the USB OTG Cable and the USB Hub etc, the setup is faster and looks less cluttered. If you are running an IoT project, you could loose the keyboard and mouse too.
IoT HAT has the same wireless radio as the Pi 3
We are using the same BCM43438 chip as that on the Pi 3 (read here) which supports both Wi-Fi 802.11n (2.4GHz) + Bluetooth 4.1 (Dual Mode – Classic and Bluetooth Low Energy) running at the same time.
You can extend the RF range easily
The IoT HAT has an on-board antenna. However if you want to increase the RF range, you can simply attach a compatible antenna to external antenna socket and flip a switch, no hacking or soldering is required.