Was this a bad play, given that I was fairly certain the villain would call? He had been playing short stacked and was happy to shove with TPWK, this strategy had been working for him

Party Poker No-Limit Hold'em, $ BB (5 handed) from (Format: FlopTurnRiver)

Hero ($26.65)
SB ($52.50)
BB ($23.95)
UTG ($18.75)
MP ($24.35)

Preflop: Hero is Button with A, K. SB posts a blind of $0.10.
UTG calls $0.25, MP calls $0.25, Hero raises to $1.5, SB (poster) calls $1.40, 1 fold, UTG calls $1.25, MP folds.

Flop: ($5) J, 8, 3 (3 players)
SB checks, UTG checks, Hero bets $3, SB folds, UTG raises to $6, Hero calls $26.65 (All-In), UTG calls $18.75 (All-In).

Final Pot: $59.40

Slightly -EV if your OC's aren't good, slightly +EV if they are, high variance either way but will probably create more action for you on your sets.

However, you have position so I prefer a call. OOP I would say this is a must shove but in position I think calling is better.

Calling with the nut flush draw getting great immediate odds with position against a bad opponent is very +EV. Pushing without fold equity is probably only marginally so.

I think he has huge fold equity, and I also think when called, his overcards are good a fairly high percentage of the time. This minraise to me says "weak top pair/2ndpair hand, or a draw".