Anything done "in a vacuum" means it was done with no interference, no influence, no disturbances. It is referring to the vacuum in space, where there is no air, no nothing.
For "programming in a vacuum", it would inferimply that a programmer is just programming by themselves. Probably need more context to know whether or not this is suppose to be a positive attribute or a negative. It could mean the programmer is doing things wrong because they aren't getting any outside help or instructions, or a good thing, because the programmer is not being disturbed and can concentrate on the job at hand.