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I think it would depend on whether there's a one-to-one match for the components in question. If you can find the exact same component (i.e., same exact specs) in both through-hole and surface-mount versions, I'd say the difference would be minimal and not noticeable. The only difference would be how the pins come out. As I understand it, it's usually pretty easy to find simple components (i.e. resistors, simple transistors, etc) in one-to-one matches for both formats. It's the complicated ICs where things get more tricky.
However, I should preface this with the fact that I can't hear the difference between metal film resistors and carbon film resistors or most brands of transistor. I can hear the difference between silicon vs. germanium, etc, but not between most brands of the transistor with the same specs. I've used both the good stuff and the cheap stuff, component-wise, and not heard the difference. I use the good stuff when I can, for durability, but mostly I save my money for a good switch, good jacks, good pots and a good enclosure because I think that has more end effect on tone and durability.
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