Each x is prime with probability 1/ln(x), each x has M/x multiples less than M, as a fraction of M that is just 1/x. Together that makes 1/(x ln(x)) with the indefinite integral ln(ln(x)). If we plug in 2^32 and 2^64 [1], we get ln(2). So about 69.3 % of all 64 bit integers should have a prime factor larger than 2^32 and therefore not be the product of two 32 bit integers. That leaves about 13 % unaccounted. Three prime factors all larger than 2^32/2, five prime factors all larger than 2^32/3, and so on cannot be packed into two 32 bit integers. Not sure to how much this will add up.

[1] The bounds are important because they guarantee that there is at most one prime factor from that range and this ensures that we are not double counting anything. If the upper bound was larger than the square of the lower bound, then we would have to worry about double counting numbers with more than one large prime factor.