running without the covers on the clutch area will allow a piece of gravel or anything else bouncing along the road to possibly get up in there.... I know, that is very unlikely but, it is even less unlikely with the covers on there.
Also, if you are rolling around under your truck with it running, you could get fingers or clothing sucked in there with out the covers on.
That said, I got the bottom one off on my 58, and could not get it to slide back in (trans mounts have deteriorated and settled, or the front of the engine is too low, I think) anyway, I have been running it for a couple years without it back on.