The real negatives are: it is expensive, it commits you to running and eventually replacing a dehumidifier, it can hide a plumbing leak until damage is done, it may require a radon reassessment, and done badly it makes moisture problems worse rather than better.
It hides leaks
This is the most underrated downside. In an open crawl space a failing supply line shows up as a wet patch you can see. Under a sealed liner, water tracks between the plastic and the soil and can run for months before it announces itself as an odour.
The mitigation is inspection: get under there twice a year and look. An encapsulated crawl space is not a space you never have to enter again, whatever the sales pitch said.
It commits you to equipment
A sealed crawl space needs conditioning, and that means a dehumidifier running for the life of the house. It uses electricity, its filter needs changing, its condensate pump will eventually fail, and the unit itself has a service life of perhaps eight to twelve years.
That is an ongoing obligation, not a one-time purchase, and any comparison against doing nothing should include it.
Radon and combustion air
Sealing a crawl space changes how soil gas moves into the house. Where radon is a consideration, the sensible order is to test before and after rather than assume. Encapsulation can reduce radon entry, and it can also concentrate it if the space is sealed without ventilation or sub-membrane depressurisation.
If any combustion appliance draws air from the crawl space, sealing it affects that supply and needs addressing at the same time.
Done badly, it is worse than nothing
Sealing a crawl space that still takes on groundwater traps the water. Sealing without conditioning holds humidity in. Both are common, both are cheaper than doing it properly, and both leave the house worse than an honest vented crawl space would have been.
The bottom line
Encapsulation is the right call for most Cape Fear crawl spaces, but it is a system with ongoing obligations, not a one-off fix. The failure modes are all avoidable and all common.
For a number against your own crawl space, use the cost estimator, or call (910) 886-2018 and we will come and measure it.