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Depends on the tone you want. Playing the lower string gives you a warmer tone and makes slides more natural.

let's say you're playing C major scale, it's better to play the D on the A string rather than on the D string? on the way down you have to mute the D string or else D and C are playing at the same time. muting's not a huge deal for a major scale but I was just wondering if there is a common standard

Playing C to D as "A(3) to D(0)" is super awkward and will sound bad unless your timing is impeccable.