Built my Leeku 1800 and Phantom in the past two days, and I have to say, I like SMD soldering more (Leeku 1800 was SMD diodes, Phantom was through-hole). I screwed up on one switch diode on the Phantom, and it was a pain to get it desoldered. Once I did desolder it, I soldered an SD diode on the through-hole pads, works fine, and I think I should ahve done that for all the diodes from the beginning.
Really if the through-hole diodes are not in-switch, I see them being a pain to remove in the future, of course you should aim to just get it right the first time.