I think it would be better if Clatrix switched to returning 1D vectors as the result of map / filter / seq etc. This makes more logical sense and would align better with core.matrix (although core.matrix doesn't place any restrictions on whether array objects are seqable or not...)
That would be a pretty big breaking change of course! So it may be more appropriate to leave this as it is at least until Clatrix gets a major revamp.
More generally though, I'd encourage the use of the equivalent core.matrix API function for getting slices and elements etc. (slice, slices etc.). This has the *big* advantage that these functions are backed with protocols, so they can be extended to arbitrary array types which you can't do with built-in seq, filer, map etc.). I think Incanter should be able to use these and eliminate map / filter etc. entirely.