Thinking it over I think there's pretty much just 3 things you can't access any more in warframe that didn't get axed back in the beta and aren't placeholder bosses getting done properly.
Deception missions, which got replaced with the more interesting Spy missions
Raid missions, which got replaced with Survival which is basically the same thing but on a timer
Arcane helmets, which are obsolete since arcanes and helmets are now two different things you equip separately
which got retcon'd into a different gun because corpus don't use bullet weapons
zha old snipetron got added back, but is only available during two events, one which recurs every like...6 monzhs or so, and zha ozher is valentines day.