Net.TeamingIgnoreShotgun can be set to ignore (Setting Net.TeamingIgnoreShotgun to 1) while EDP (Enhanced Data Path) is enabled on an ESXi host. This configuration will not cause any disruption.
Net.TeamingIgnoreShotgun configuration does not talk to the driver stack, rather to software side. This has no relation with EDP.
There are no issues about co-existence of EDP as well as Shotgun as both operate at different levels. You can enable/disable shotgun settings in the environment where EDP is enabled without any interruptions.