The pomerium was not extended frequently. Discounting the supposed extension of the pomerium by Servius as legendary, there are only four certain extensions of the pomerium, by Sulla, Caesar, Claudius, and Vespasian. A fifth extension by Augustus is possible, but not to my knowledge generally accepted. Tacitus says Augustus extended the pomerium, but Augustus makes no mention of it in the Res Gestae despite the massive symbolic value it would have had for his vision of refounding Rome, and there's no evidence of an actual extension. Note also that the lex de imperio lists only Claudius as a precedent for granting Vespasian the right to extend the pomerium, not Augustus. Hadrian probably did not extend the pomerium, but only renewed it. Extending the pomerium was a fossilized ritual of the kings, and could not be done for much of Roman history without very special circumstances. And after Vespasian the emperors, despite knowing the significant symbolic value extending the pomerium had, did not follow his example. There were only four certain, possibly five, extensions to the pomerium in a good thousand years, all happening within only about a century.

We do not know the circuit of the Republican pomerium, and we only somewhat approximately know the circuit of the pomerium under Claudius and Vespasian. We know that the Republican pomerium did not include the Aventine, even though the walls did. We don't know what the extensions by Sulla and Caesar were exactly, but they cannot have been terribly large. It's possible that they went over some burials. But extending the pomerium over burials doesn't seem to have bothered anybody. The Twelve Tables don't actually say that there can be no graves in the pomerium, they say that the dead cannot be interred in the city. That doesn't seem to mean that graves already in the city limits have to be removed, and of the city's earliest necropoleis the one in the forum was within the Republican pomerium. The tombs are still there, you can see the excavations if you go to Rome. By and large, though, this doesn't seem to have been a problem for most of the Roman period: tombs were typically constructed outside the walls, not the pomerium, along the roads that necessarily ceased to exist at the city gates. The Esquiline cemetery, for example, was on the other side of the Servian circuit, as were the popular and more expensive tombs lining the Via Appia. But there seem to be cases of existing tombs being incorporated into the expanding pomerium. Claudius added the Aventine, where there are some tombs (the colossal Pyramid of Cestius is, if I remember right, outside the Imperial pomerium, since it overlaps with the Aurelian circuit). I'm no expert on the archaeological location of Roman urban tombs--they're much more interesting, in my opinion, for their inscriptions and monument types--but last time I checked there were tombs on the left bank of the Tiber, which was probably incorporated into the pomerium by Vespasian. And for whatever it's worth, the Romans built on top of tombs all the time--Maecenas built his massive gardens directly on top of the Servian circuit and the Esquiline cemetery on the far side of it.