Acceleration/thrust is a constant, regardless of the presence of an atmosphere. The issue you are referring to is drag. Drag decreases the efficiency of thrust, so more thrust is required to get the same performance if you are encountering drag.
As acceleration increases, and you have a denser atmosphere, you can get to a point where drag increases to the point where you are literally running into a brick wall. Plus you get increased thermal bloom as well as stress on your airframe. This is why Traveller gets it wrong showing ships that would work in a subsonic environment, but not in a supersonic one, let alone anything faster (at least at lower altitudes). Anything moving faster than Mach 1 is supersonic, and past Mach 5 is hypersonic.
The space shuttle converted it's speed into Mach numbers when it begins its descent. It starts out at roughly Mach 25 in the very upper levels (thermosphere), then does a braking maneuver over the Pacific as it transitions through the mesophere/stratosphere to bleed speed through drag. It's a very specific maneuver designed to take advantage of the properties of drag. While technically it doesn't have acceleration on the way down, it has a great deal of inertia that, combined with lift, its' able to do a controlled glide.
A Traveller ship, with antigrav for lift would not need to do any of that and would not have any of the thermal / hull stresses that the shuttle has. But it would still be subject to drag. Because it has antigravity it could do reentry at any angle and orbital speed, thus skirting the issue of lift vs drag. That also means it has no need for higher speed in an atmosphere (so the non-aerodynamic ships could literally float down to land quite efficiently at a measly few hundred Kph).
As acceleration increases, and you have a denser atmosphere, you can get to a point where drag increases to the point where you are literally running into a brick wall. Plus you get increased thermal bloom as well as stress on your airframe. This is why Traveller gets it wrong showing ships that would work in a subsonic environment, but not in a supersonic one, let alone anything faster (at least at lower altitudes). Anything moving faster than Mach 1 is supersonic, and past Mach 5 is hypersonic.
The space shuttle converted it's speed into Mach numbers when it begins its descent. It starts out at roughly Mach 25 in the very upper levels (thermosphere), then does a braking maneuver over the Pacific as it transitions through the mesophere/stratosphere to bleed speed through drag. It's a very specific maneuver designed to take advantage of the properties of drag. While technically it doesn't have acceleration on the way down, it has a great deal of inertia that, combined with lift, its' able to do a controlled glide.
A Traveller ship, with antigrav for lift would not need to do any of that and would not have any of the thermal / hull stresses that the shuttle has. But it would still be subject to drag. Because it has antigravity it could do reentry at any angle and orbital speed, thus skirting the issue of lift vs drag. That also means it has no need for higher speed in an atmosphere (so the non-aerodynamic ships could literally float down to land quite efficiently at a measly few hundred Kph).