You certainly don't need to use a conduit instead of a cable to satisfy the requirements of the NEC, or more importantly the AHJ (authority having jurisdiction). I'm finding myself to be considered more and more of an "old timer" even at the ripe old age of 48. That's sometimes because my obvious prefferance for metallic wiring methods and use of conduits and raceways (I like using the Chicago Electrical Code),,,, but even I am changing a bit. It is in fact becoming more and more common to use cables instead of conduits (raceways) because the continual improvements of the material used in cables, as well as the (percieved) istallation labor costs. If your blower is rigidly attached in a fixed location, "sealtight" or other "flex) is quite typical.
"S.O. cord" is more common for fractional and small integral horsepower motors between the local disconnecting means and the motor itself, when the motor vibrates and moves a bit, such as a variable sheave or similar belt drive. If your installation is in a location which is exposed to damp conditions at times, and condensation may form, a cabled connection is far prefferable.
I've replace more than a few "sealtights" in HVAC and refrigeration, outdoor, or wash-down installations which had rusted to nothing inside and didn't provide any useful shield or ground continuity (or frequently mechanical protection). Why use "flex" at all? Construction; "pull 'em long and use the cuts for the whip". Just the same THHN wire as the rest of the circuit keeps it simple. Heck I've even seen some really lousy foremen have stuff trimmed-in with the same solid #12 they like to use throughout a job. (I can really get going on that kind of stupid stuff!)
Cable is not always sized the same as conductors for general wiring, as it has it's own heating tolerance and characteristics. Actual SO cord is obsolete. There's some very good cable available as far as durability, oil, moisture, chemical resistance, all-temperature flexibility, limitation or elimination of moisture migration, etc, etc. By all means use a good quality, properly sized connector for terminations at the motor terminal box and the other end. Some amazingly good non-metallic ones of these are now available also.
Please let us all know how this works out for you! and don't forget faq731-376