We are given the number:
\[ 2^4 \times 3^5 \times 10^4 = 2^4 \times 3^5 \times (2 \times 5)^4 = 2^4 \times 3^5 \times 2^4 \times 5^4 = 2^8 \times 3^5 \times 5^4 \]
Now, to count the number of perfect square factors, we consider only the even powers of each prime factor.
\[ \text{Total perfect square factors} = 5 \times 3 \times 3 = 45 \]
Since 1 is also included as a perfect square factor, we subtract it:
\[ \text{Required count (excluding 1)} = 45 - 1 = \boxed{44} \]