I can roll with it as just a game balance/don't blow up the ships too fast sort of mechanism.
I can even see it being reasonable for streamlined ships re: reentry/scooping and minimizing protruding/weak spots in the hull.
In a sense, carriers 'subvert' the rule by hosting several times the one turret per 100 ton rule, so you always have that option to load up for the battlefield.
As a matter of refereeing, I would probably let players with a blowtorch and more budget then sense cut up a hull and install rule breaking numbers of turrets, all the while warning them 'this is not best practice' 'your ship's architect resigned the commission rather then have his name associated with the project' etc.
Then impose all manner of hull fractures, overheating, cascade power failures and extra internal damage from turret hits due to improper bulkheading, etc. all during combat or reentry.
Don't forget all those turrets need gunners, the personnel and stateroom/life support costs go up to and are a practical limit.
And of course the deadliest threat of all, Annual Maintenance Certification. Ya buddy, try and service that loan debt when you are disallowed from accepting full price legal passage tickets and cargo and have to skulk around X starports and deep space drops accepting underpriced/highly illegal cargo to eke out an existence.
You could go a different route, it's just a convention to keep people from having destructive 800 ton pocket battleships and its illegal and shoot on sight to be so well armed.
But the Excessively Nasty Empire Next Door has no such qualms...