There's no native way of adding new icons to the game except totem icons that appear in the character sheet. Custom totems are listed in /data/totems in a UGCname.tml.txt file (see the Seattle.tml.txt file in the Seattle Content Pack for reference), and their icons must be in \art\totems folder as 128x128 png files of the exact same name (case sensitive) as listed in the aforementioned tml file. Icons for totem abilities are still restricted to the ones available in the game resources.
There is a mod available for adding custom icons for items and abilities. Place the 128x128 png format icons in a new \art\customui folder in the Content Pack and then assign those icons by the exact png file name (without .png) to item sheets and ability sheets. Weapons need additional stroke and fill icons. For more details, read the instructions in the mod page.
The mod must be distributed with the UGC or be made a requirement in order for it to work.
SRR Electric Mod for Shadowrun Returns
SRR Electric Mod for Hong Kong
Custom icons in-game.