Does Araquanid's "Bubble Trap" attack get its bonus damage if the Pokemon that used "Bubble" on my previous turn was Knocked Out or is no longer in play?
Yes, you get the bonus damage. The effect of "using Bubble" is on the player, not on the Pokemon.
Source: Forbidden Light FAQ (2018-04-20), TPCi Rules Team (2018-05-03)

Relevant cards

Note: All applicable cards may not be listed below.
SM6_33