[...]but then they are walking around in constant bullet time, which may not strictly speaking be good for the mind or for one's ability to judge speeds and therefore things like the force of incoming objects[...]
Which would be the same for synaptic boosters which don't have an on off state and have no side effects mentioned... so there should be no side effects for wired reflexes too.
The only thing that the RAW "must be activated" means is that at right after the implantation you need to say "I activate my wired reflexes" once and then be done with it...
Ofcourse many groups play it like you need to activate it each encounter/scene or whatever, but this is just a thing that needs be made clear at the table how you play it...
There could be numerous reasons that require you to activate it each time instead of activate it once and then make it last the rest of your life,
a) it messes with your relax/sleep cycles which would require you to turn it off/on it each evening/morning or each time you'ld want to relax (smoke a cigar eat something chill in a hammock...)
b) it has safety measures or a limited supply of whatever (power maybe) that deactivate it automatically after... I dunno a minute? (20 combat turns) or a not given amount of time that is essentially end of combat/end of scene
c) it could have long term side effects if you always had wired reflexes at the on state
all of these are houserules and the fact, that there is a switch but no explanation is kinda a copy/paste thing from 3rd ed
The initiative boosters with all their quirky rules like "works with no other initiative improvement" are in a state of errata need and we can only hope, that Shadowrun 5 finally clears it up.