Does disabling the prompt to enable two-factor authentication on an iOS device disable future prompts from appearing?

You cannot guarantee that the user will not be prompted in the future.

There's a continued development in security and the need for preventive measures. Today two-factor authentication is absolutely crucial and wide-spread, 25 years ago it was only used by the few.

Apple some times "moves the bar" by changing the minimum security requirements. In those cases, they could start prompting user's again for enabling two-factor authentication - or even requiring it entirely.

For example, not so long ago the requirements for developer accounts were changed so that these users must have two-factor authentication enabled (also affects apps such as TestFlight, App Store Connect, etc.). These users were notified in advance that this requirement would be instated.