I've never thought that Dexter's monetary stuff was a plot hole. He makes at least decent money - several articles suggest that he would make above $60,000 - $80,000 given his experience and his location. He does nothing at all with his money aside from bare necessities and property maintenance. It's reasonable to think that he's been working for something like 10-15 years, so his apartment could be paid off. Harry wasn't poor either - so he could have a sizable inheritance there and another one from Rita. You'd be surprised how far your money can stretch if you only spend on the necessities.
Dexter more recently inherited a house from his real father, plus he has whatever estate Rita left (equity in house?) plus insurance money from her murder, though this latter has never been mentioned AFAIK.