Experience I had with one of my 750 mates;
Fitted the straight-through pipes, marveled at how sleek the bike looked, awesome sounds. Noise drowned out just about everything else, engine seemed a lot stronger... headers loosened, tightened, repeated about 2 dozen times with numerous replacement header gaskets installed. Welded cracked header, replaced header gaskets... about a dozen times. Fast forward a couple of years, the headers looked quite shitty, but there was a bike event coming up, so original system was re-fitted, looked a bit better, despite the rust it had gathered in the meantime, hanging from the rafters in the shed. Visited the bike event, asking himself all the way "WTF did I bother with those pipes in the first place?" Total time span about 4 years. Eddy hardly recognised his engine with the OE system re-fitted, smooth, civilised with loads more grunt. No more hassles with loose headers either...
The original silencer(it is actually more than just a balance tube) is a rather clever design, very low restriction and allows each cylinder to breathe into both silencers, enhancing low- and mid-range torque. About the only drawbacks might be limited cornering clearance, along with a bit of hassle when the silencer needs to be removed during servicing. I have managed to ground the silencer of my GTL only twice in the past 20 years, and don't feel limited while cornering at all(including chasing and overtaking GS Beemers down the Grossglockner

Not enough steam to keep up with them uphill...). Don't consider the bike being not loud enough either, by todays' standards at least. It's a rorty, but civilised beast.
The exhaust system relies on a support mid-way along its length, otherwise it will self-destruct. If the silencer really needs to go, at least fit some sort of support for the headers near the footrests, or fabricate a "H" tube to connect the headers, similar to Guzzi Lemons or Ducati bevels.
piet