Can SMPS based preamps/amps sound organic ?

but I always seem to hear some kind of switching noise which comes through as "digital" sounding.

hmmmm.....I wonder if you are imagining this? How did you trace/pinpoint the "digital" sound to exactly the SMPS in the preamp/amp?

I wonder if there are any designs using SMPS that can actually sound natural and organic ?

sure! At RMAF2013 I heard the Rowland 625 driving a Raidho stand-mount & it sounded very good. For the limited time that i was in the room on Sat & Sun I could not find any obvious faults. I, of course, discounted the fact that the Raidho, no matter how good, could not reproduce deep bass.
There’s been rave words said about the Merrill Veritas amp which also uses a SMPS power supply. If I'm not mistaken Bel Canto Black is another example.
There must be many others out there.....

SMPS used for convenience?
Maybe. At one point i was talking to a well-regarded engineer at a class-D amp manuf & was informed that SMPS in amplifiers are just about coming into their own. Their fault, as you stated, was high(er) output noise for audio applications. We already used SMPS in other audio applications such as cellphones as the audio quality does not matter as much (different application & diff specs). I was informed, by this engineer, that the highlight of the Hypex NCore N1200 amplifier module was its SMPS. And, the final goal for any class-D amplifier was to use both a SMPS power supply + SMPS amplifier module.

I don't have solid answers for you, but I do have an experience to share which I believe is a partial answer. 
I wanted a better dac that got me into better ES9018 chip.  I purchased a kit and did all the work.  After speaking to an old friend who is fairly well known years gone by as a competent designer,  he convinced me that done right, there was nothing wrong with a switching supply.  Being a beyond frugal,  okay, cheap person,  I had found a TV/DVD switching power supply that had the exact voltages that I needed for my dac.  I purchased this,  put it in,  fired it up.... IT WORKS... Fast, smooth, but had a glare that I couldn't deal with, waited for weeks to break in.  Still glare.  Took it to my buddies house,  he took measurements,  measured again and ended up building a filter network for the power supply.  Wholey Moley what a difference.  Glare is gone,  detail improved, weight/authority.  I became a happy camper quickly. 
Another friend purchased a Pass/First watt clone that Nelson offered up on DIY.com..  My buddy told him the same thing... Again, DONE PROPERLY a switching supply is fine,  even on a traditional amplifier. In his case,  he had already purchased 2 transformers and ran that direction.  I'm a speaker guy,  but I'm sure one of the amp guys out there will chime in and tell you why. 

My Jeff Rowland 625 S2 uses SMPS and it's the best, most natural sounding amplifier that I've ever owned.