In Character - Inventory - Accessories, upgrading an accessory doesn't increase the bonus displayed. It appears to be working, the numbers change elsewhere, it just doesn't populate the new values onto this particular screen.
For example, a level 2 Printed Circuitboard appears to be adding +3 to my Hack score during missions, but only displays the +2 on the character-inventory screen/tab. (The hover-tooltip on that page DOES show the increased value, however.)