John,
I haven't rooted up too many plants, and if I do it's only a couple crypts or stems at a time. I quickly syphon up the soil that's pulled up. I haven't had any algae issues so far myself after doing this. I would think it could get pretty messy if you tear up the whole scape though.
The only 'con' I've had is the initial bloom of cloudy/green water for the first couple of weeks when you set up. With daily/every other day water changes this clears up without much issues over time.
__________________
|