trying to represent a flush OTR, unexpected call by opponent !

I would fold J9s at my full river tables. However, J9s call at shorthanded seems reasonable. I agree with how Hero and Villain played this hand up to the River. Villain played it well with a smooth 13 BB River call with TPTK. However, Hero needs to pot bet to truly represent a flush. That is an expensive, but sometimes profitable line. I personally don't like representing a flush in this scenario because it cost a lot to do so properly. I would have checked the River with the second board pair and weak kicker.

(You never check OTR to trap someone, it is either fold or call.

It may be that you never check on the river to trap however what about your opponent! I am sure that there are others who would check on the river to induce a bluff/trap, I know I have.
Perhaps your opponent would have folded if you represented a flush but as you would have needed runner, runner to hit that flush what portion of your range on the river in this hand has a flush?
I suggest you have more missed flush draws in your range than made flushes and with such a small bet from you your opponent may have called simply thinking his K kicker was good.
What range did you put him on that you thought he would fold to such a weak bet? He raised pre, bet the A on the flop and again on the turn, both times OOP. Your only chance to win this pot was to get him to fold the river so more consideration to his range and what bet you need to make to get him to fold out that range is needed for a bluff to succeed here.
"my assumption was that he was scared by the last spade which made the board flushy" - no mention of what range you put him on that he would play as he did, just an "assumption" on your part that he was scared of the flush - for all you knew he may have been betting with the AsKs or AsXs and checked to induce your bluff.
I agree with srichards that as played a check behind on the river is the way to go.

Tough to represent a backdoor flush, because most players will fold this on the flop and than you only represent a hand like A♠:Q♠: . Also you are playing on NL2 and than it's tough to represent hands with in mind most players have no clue what they are doing. In this scenario I would fold pre-flop against most players that raising 4x with in mind your J9s isn't strong enough against his raising range.

Cheers,
SDK1987