I would assume ram. Instead of replacing the default theme, winterboard overlays the theme without overwriting / changing your default theme. Im not sure how much ram the ipad mini has, but my iphone 5 shows 500-700mb free under normal use. I use kill background to kill running apps. It has a nice icon in the multitask dock that you can tap to close all apps. My ipod touch 4g shows 125+mb free but with running apps it goes to 60ish and gets slow.
I currently use a theme to make all my menus/ keyboard/ settings orange tinted and havent noticed a significant drop in free memory. Im assuming some of the crazy themes which change all your icons and have more complicated designs can consume more ram. Mine is basically what an orange apple theme would be. Close to default but orange instead of grey/blue. I tried not to go crazy with all the unnecessary tweaks since I want my phone to be quick first and foremost.