Indeed everybody has nowadays EP for Vel Nexus, but you cannot fit it without costs.
EG tackler with Nexus has strong limits on other fit, nexus as well costs you energy, there are several bots not beeing able to fit/use masking and nexus together, so oyu have to choose.
With this argument, we could remove weapons from equipment, as every Kain/Artemis/Tyrannos has them equipped and you cannot enter Pvp without having at least one bot with them fitted.
The Navigation extension was something complete different, as it had only few EP spend and no other side effects.