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From my (limited) experience - using indexes instead of pointers has additional advantage - it makes it super easy to serialize/deserialize arbitrary graphs of objects.

Save game if you use index for referencing objects = one fwrite call.

Save game if you use pointers = a lot of pain.

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Pointers can be easily mapped from and into integer indices or file offsets in-place, so there is no big difference really.

I think it is generally not a good idea when in-memory representation of objects is identical to the serialized representation. This approach tends to backfire in a number of ways, such as format incompatibility between software versions, or hardware architecture differences, so it is always better to assume that your serialized representation will be different from in-memory representation.

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