I can't speak for any other engines, but in SpiderMonkey a BigInt is a GC-managed object with a one-word header containing the sign bit, the length, and some GC bookkeeping bits, along with a second word that is either a single inline 64-bit digit, or a pointer to an array of 64-bit digits. So the memory overhead of a BigInt that fits in 64 bits is "only" 2x, but doing math with BigInt requires more work than a native integer because it needs to handle larger numbers, manually manage sign bits, and so on.
(https://searchfox.org/mozilla-central/source/js/src/vm/BigIn...)