>>23391969 (OP)>>23392123 is one part of it, you immediately may need to use fiber optic drones like the EF was already using with their conventional missilesin the OYW to use suicide drones, or alternatively you need to have those suicide drones work akin to relatively uncommon self-guided UC missiles and have them track things like heat signatures or the target by eyeball or so forth.
Mobile suits themselves already have several layers of protection drones need to get past. One thing we need to remember is that with enough protection a single suicide drone is actually not always enough for a vehicle like a tank, given it is protected adequately, so the drone needs a relatively hefty warhead. Zakus have been shown to have anti-infantry flechette weapons which could be used against drones in 08th MS Team and MS IGLOO, which would presumably be repurposed to be fired against drones. MS like the Gundam and other EF machines tend to have head vulcans, which would also be an immediate option and which can be effective against drones of certain types. Presumably, with the right sort of ammunition and tracking equipment, head vulcan effectiveness against small drones could be dramatically increased.
Mobile suits are relatively maneuverable, so many drones used against them might need to use the tractic some interception quadcopters use as-is of flying extremely high into the atmosphere and then flying down onto the MS, though this is usually a counter-drone tactic as opposed to an actual aircraft or ground vehicle interception tactic and would likely not be as effective against MS actively moving via their jets or hovering (e.g. common jumping, Dodai/Base Jabber flight, Dom hovering). This is complicated, however, by the fiber-optic requirement. It would presumably be a good idea to attack MS while they are parked using bomber drones as opposed to suicide drones, but just like in the current war this is countered by concealment and defensive construction.