I think it depends on the situation. If you have a long term operation that requires crews be maintained on a hot stand by, where performance and completion clauses penalize you for failure to perform, including a fee schedule for weather or other delays is prudent and justified.
To require crew and equipment be maintained in a status that has them instantly available for operations when conditions make operations possible means you have to keep everyone and everything close to the operation. Crews cannot be expected to bear the costs of things like out of town lodging and vehicle rentals unless they are being paid, and few contractors can afford to pay those costs from a base contract fee, or out of pocket. It takes very little down time without pay for a good crew to look elsewhere and accept gainful employment. You either pay a reduced stand by rate and per diem or lose them. If they were providing their own equipment you lose that too.
If you hired people as employees you have federal labor laws to contend with. The time an employee is required to be available for work, working or not, is compensable time. If you require they remain available on days not working, limiting their movement, all that time becomes your time as the employer, not their time.
The cost of weather and administrative delays is an essential part of large operations. Small day to day stuff is not a big deal as those you can walk away from, but if you are subjected to performance penalties you darn well need to cover your bases. Such clauses are written into contracts to protect the client and reduce their costs when time limits are exceeded, at your expense. We are in business to make money, not finance the operation of the primes.