This'll allow for multiple laser strikes in a single bombing run, or even something as straightforward as lasing and bombing one target while deploying a second bomb to be JTAC/buddy lased.
In the case of the 45 I'd implement it by adding a new mode to the toggle at the bottom left of the SMS screen. The pilot would tap the mode toggle until it says SEEKER, select the munition they wish to configure and then tap in the code their buddy is planning to use. Weapon switching now treats that bomb as its own weapon group (any manually configured munitions with the same laser encoding are grouped), and it is clearly indicated by the SEEK/encoding/LOAL indicator on the HUD. Shipwide encoding would work as it does currently (not pictured; this is an old screenshot from the wiki).
Lowtech encoding would be performed via the Equip menu; select the munition and you have the display with the various munition configuration options (e.g. MADDOG for the 120). A new 'SEEKER' option is added here, when selected can take input from the numpad. Weapon switch grouping and HUD indications would work pretty much the same way as above. I realise Not as quick as the glass cockpits, but I can't think up any other way that is quite as clean for per-munition encoding.