Come to think of it... I don't think it will have much performance hits at all.
Because bignums by nature, will have a very large base, say a base of 65536 or larger for which is usually a maximum possible value for traditional fixnum and integers.
I don't know how large you would set the bignum's base to be but if you set it sufficiently large enough so that when it is used in place of fixnums and/or integers, it would never exceeds its first bignum-digit thus the operation will be nearly identical to normal fixnums/int.
This opens an opportunity for optimizations where for a bignum that never grows over its first bignum-digit, you could replace them with uber-fast one-bignum-digit operation.
And then switch over to n-digit algorithms when the second bignum-digit is needed.
This could be implemented with a bit flag and a validating operation on all arithmetic operations, roughly thinking, you could use the highest-order bit to signify bignum, if a data block has its highest-order bit set to 0, then process them as if they were normal fixnum/ints but if it is set to 1, then parse the block as a bignum structure and use bignum algorithms from there.
That should avoid performance hits from simple loop iterator variables which I think is the first possible source of performance hits.
It's just my rough thinking though, a suggestion since you should know better than me :-)
p.s. sorry, forgot what the technical terms of bignum-digit and bignum-base were