I've said this before - but its always worth repeating. The issue is not the top box as such, it is the fact that any solid lump in a fast airflow will result in dirty air eddying behind the solid lump. You are the solid lump - no offense intended. The air whips around your back from one side and then the other - you don't feel it unless you have a very loose jacket on. But your top box gets the brunt of this and it gets battered from side to side. The Honda top box is designed to move laterally on its fixings to cushion some of this effect. But the best ways to get rid of it are either remove the top box or fit a pillion. Riding two up with a top box it doesn't happen - the air cannot eddy behind you becasue there are three solid lumps, all in a neat line. The slipstream cannot start to break up into eddies until it has gone past the top box. It is no longer your problem.
It also becomes less of a problem the more you ride. Big gust of wind from the side - always a bit un-nerving - but the natural instinct is to grip the bars which prevents the bike from self correcting. It has two massive gyroscopes spinning under the mudguards - they want to go back to where they were. Gripping the bars prevents them from doing so. I suppose it is like standing on a sailboard, and then suddenly they do. The ST1300 is a big bike with a big surface area. It catches the wind and you get used to not having that gripped reaction to it. A bit like me at the moment desperately trying to unlearn the natural countersteer correction on my new-to-me trike. I'm getting there but its taking time.
I saw an extremely low mileage ST1300 the other day £6000. I wanted to buy it - but there was a reason for buying the Spyder - and I just have to go through the processes - most of which we have all done - learning to walk, ride a bike, skateboard, ski, bike and sidecar, rock climb, canoe, sailboard, big solo bike, big faired bike in cross winds, walk again, trike, mobility scooter ! You get the idea. I was trying to find something to put in between those last two. Oh dear !!
And the bow wave created by big trucks ? Ride out 'wide' (ie on the outside of your lane) and as you get level with the cab gently countersteer towards the centre of your lane. If the bow wave hits you - you are already leaning into it - so you end up going straight ahead. If not, no problem you just straighten up so that you don't cut him up.