With rockets like the Atlas 5 (flown by ULA), the rocket is assembled vertically in a tall "hanger", and is then rolled out to the launch pad, remaining in the vertical position.
The Falcon 9 is assembled rolled out to the pad horizontally, then it raised into the vertical position in preparation for launch.
It can be more complicated to design satellites (esp satellites that have large optics in them) to deal with gravity in two different orientations.
Complicated and less weight-efficient. Designing a structure for gravity/g/force in one axis is wasteful enough. That strength is useless once in space. Horizontal integration means the structure must be strong in two axis: double waste. It might not matter when you are launching cubesats, but in a spy satellite the size/weight of a bus that extra reinforcement means sacrifices in many other areas.
But it's more economical, money-wise, as Russian launchers history shows. In general, American rocket school tends to have better mass efficiency but less economical efficiency that Russian rocket school.
"When he wants more thrust, Ivan doesn't look for a fancy propellant with a higher specific impulse. He just builds himself a bigger rocket. Maybe he's got something there." - J. Clark, Ignition! https://library.sciencemadness.org/library/books/ignition.pd...
Of course the point was that one can use simple and crude solutions, or effective and sophisticated ones. Another example would be that in Russian rocket engines pumps tend to be put on the same axis as the turbine, so frequencies of turbine and pumps are the same and some of them can be non-optimal. In American tradition one uses gears, which makes both turbine and pumps (more) optimal, for the cost of gear mechanism. Practice shows that both approaches can work, but, just as with vertical assembly, which requires a tall building or a vertical transportation of a rocket, some ways look simpler than others. Simpler not necessarily better - but in rocket assembly it's probably cheaper to do it horizontally.
It's a bit more than cubesats. Nearly every satellite is or can be fine with horizontal integration. Witness every SpaceX and Russian payload ever launched.
Only exotic (presumably optical) sats from three-letter agencies really demand it, and even then we don't know if they really need it or would rather just spend the money to make it the launcher's problem rather than do a redesign or evaluation of their system.
SpaceX undercut the market price for space launches by nearly 70% in 2010, and has averaged a launch every two and a half weeks for the last four years.
Usually by truck for at least part of the journey (airplanes, boats, and trains are also commonly used). They are carried in custom built frames that hold them in the correct orientation. The frame is then surrounded by a sealed box that keeps the satellite clean, and with the appropriate climate controls (temperature, humidity, etc).
Here's a good overview of the process (though in this case it's a satellite that can safely be transported in multiple orientations): https://qz.com/1346279/big-plane/
It just seems to me that it would need to be horizontal, and likely encounter greater stresses during transport than during a tightly controlled horizontal assembly process.
ULA basically built a portable clean room around the tip of the vertical rocket, to put the payload on top. Because the rover has to be free of earth organisms.
The Falcon 9 is assembled rolled out to the pad horizontally, then it raised into the vertical position in preparation for launch.
It can be more complicated to design satellites (esp satellites that have large optics in them) to deal with gravity in two different orientations.
Atlas 5 "roll out": https://spaceflightnow.com/2020/07/28/photos-atlas-5-rolled-...
Falcon 9: https://www.youtube.com/watch?v=TYJuHuhPxGU
Bonus video, Smarter Every Day chatting w/ the CEO of ULA while watching a Delta IV Heavy roll out to the launch pad: https://www.youtube.com/watch?v=OdPoVi_h0r0