I reckon, yeah.Especially digital downloads of retail titles, they should definitely be cheaper than physical versions. I mean there's no packaging/media, we pretty much have to provide our own storage space for the download, you're losing the ability to sell the game in the future, Nintendo's safeguards for digital content aren't exactly great, etc...
I think if a game has an RRP of £40 it should be at least £30 in the eShop, not £50+ which has often been the case.
Nintendo's presence at retail is shot to shit at this point, so they shouldn't be concerned with undercutting retailers now.