I guess that would depend on the command but I would say that any performance penalty for the abstracted Salt version would be minimal. A few more operations for conditionals and the like may have some impact won't make much of a difference.
Doing a very un-scientific test by timing the same operation in 2 different ways on the same minion come in nearly identical.
Personally, I try to always use the abstracted version if possible to avoid a re-write should I want to re-use a state for another OS. A minor performance penalty (even if there is one) is worth the abstraction to me.
~ $ time sudo salt 'REDACTED' file.makedirs '/tmp/test1/'
REDACTED:
None
real 0m0.645s
user 0m0.481s
sys 0m0.057s
~ $ time sudo salt 'REDACTED' cmd.run "mkdir /tmp/test2"
REDACTED:
real 0m0.642s
user 0m0.495s
sys 0m0.042s