Assuming that you are using a good lens profile, say one that Adobe has predefined in Lightroom, are there any downsides to automatically applying the appropriate lens correction profile when the photos are imported?
The lenses I am shooting with appear to be correctly identified by Lightroom so there is no risk of the wrong profile being applied.
It seems to me that applying it would give you the most acurate representation of what ever it is you are photographing.