I use Ekko to play Clocktower Guardian with discount. He dies at the end of the turn and I Play houndwards with two power. Then there is a time warp on top of my deck. Do I get an extra turn?

Yes — a Time Warp played off Clocktower Guardian's Deathknell at end of turn still gives you an extra turn, but only if you can legitimately pay for it: "ignoring its Energy cost" zeroes just the 10 Energy, and Time Warp still costs 4 Mind power (rule 356.1.b.2). Two power isn't enough, so with only 2 floating the play is illegal and the Time Warp simply stays banished.

I couldn't find a card called "Houndwards" — but if whatever you played there drained your rune pool, that's what decides it: you need a full 4 power available after the Guardian dies.

If you do pay it, the timing works fine: the Guardians's Deathknell resolves during your End of Turn step (rule 317.1.a), and Time Warp's additional turn is inserted directly after your current turn in the queue (rules 735, 738), so you take it before your opponent's next turn — nothing is lost for casting it in the ending phase. Note the "Kill me at end of turn" from Ekko's discount doesn't stop the Deathknell; being killed at end of turn is exactly what fires it.