Ach, all die Aufträge, die ich schon für sie erledigt habe. War kaum einer drunter, der sich für mich gelohnt hätte.
Given that the sentence starts with war instead of wäre, I would be tempted to match the tense and say instead:
Ach, all die Aufträge, die ich schon für sie erledigt habe. War kaum einer drunter, der sich für mich gelohnt hatte.
The Konjunktiv II indicates hypothetical or counterfactual mood. It is used because none or very few of the jobs actually paid off.
In German, the Konjunktiv can be used whenever appropriate, which depends on the contents. There's no "sequence of tenses", or need to match it to other verbs in the same sentence.
And you wanted to match tenses in the in the indicative, to match the past tense of war, you'd have to use Perfekt or Imperfekt, not Plusquamperfekt:
..., der sich für mich gelohnt hat.
..., der sich für mich lohnte.
Perfekt is the better choice, Imperfekt sounds really old fashioned here. Plusquamperfekt doesn't work, because it indicates that something happened before the action in the simple past:
Nachdem ich den Auftrag erledigt hatte, bekam ich meinen Lohn.
Assuming that there is no further context here, the subjunctive does not make sense here. The first sentence states that the speaker actually did the jobs. Thus they actually did not pay off. Hence it should be hat and not hätte. This is analogously to English, where you wouldn’t use would in such a situation:
Alas; all those jobs I did for her – barely one amongst them that paid off for me.
However, in a different context, if the speaker did not actually do the jobs, a subjunctive would make sense here (and tenses still would not match):
All die Aufträge, die ich abgelehnt habe. War kaum einer drunter, der sich für mich gelohnt hätte.
All those jobs I declined – barely one amongst them that would have paid off for me.
Here the jobs the jobs neither paid off nor did they not pay off for the speaker, since they were never done. But if the speaker had accepted them, they would not have paid off. Thus speaking about the pay-off is hypothetical and this is why the subjunctive II must be used in this context. You can also see this by writing down the implicit, unfulfilled condition:
All die Aufträge, die ich abgelehnt habe. War kaum einer drunter, der sich für mich gelohnt hätte, wenn ich ihn angenommen hätte.
All those jobs I declined – barely one amongst them that would have paid off for me, if I had accepted it.
Inserting such an implicit condition does not make sense in your context.
Finally, note that an additional context may explain the subjunctive in your example. For instance:
Als wäre ich nur am Geld interessiert! Ach, all die Aufträge, die ich schon für sie erledigt habe. War kaum einer drunter, der sich für mich gelohnt hätte.
As if I were only interested in money! All those jobs I did for her – barely one amongst them that would have paid off for me.
Here the hypothetical context is that the speaker is only interested in money. In this context the jobs would not have paid off. However in reality, non-monetary aspects (e.g., love, ethics, favours) made the jobs pay off again.
Short answer:
War kaum einer darunter
says that there was none, and when there was none, but you anyway try to speak about it, as in this example:
der sich für mich gelohnt hätte
you speak about something which does actually not exist, something hypothetical, something irreal, something merely imagined.
And there you are: this is not real, so you use 'Konjunktiv'.
At least in educated language. But people who can use this correctly a hard to find nowadays.
