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As the name suggests, the choice was made to implement numbered objects as integers, and not as pointers. In standard-conformant C, integers can be safely checked for validity, while pointers cannot.
There are efficiency tradeoffs between pointers and integers but they are complicated, and they go both ways. Pointers can be faster, but integers can be used as indexes into more than one data structure. Which is actually faster depends on the design. Integers allow for a more flexible design, so that once the choice is settled on, careful programming can make them a win, possibly a very big one.
The approach taken in Libmarpa was to settle, from the outset, on integers as the implementation for numbered objects, and to optimize on that basis. The author concedes that it is possible that others redoing Libmarpa from scratch might find that pointers are faster. But the author is confident that they will also discover, on modern architectures, that the lack of safe validity checking is far too high a price to pay for the difference in speed.