generally it takes one or two knife cuts to take out a water lily, perhaps you are confusing them with lotus that have tunneling rhisomes, or then theres the nuphar's which tend to spread if neglected for a long time.
There are a hundreds of water lily varieties which are not invasive and take maybe a pleasant afternoon a year to tidy up. How anybody could be put off using good waterlilies by the notion of them costing a thousand bucks for pruning a well chosen plant might be a tad unrealistic, and probably doesnt know much about aquatic plants beyond chucking chemicals and inflated bills at them.
Regards, andy