Rearrangement Inequality
Pyth, 29 28 bytes

M/*FPJm*F.!MhMrd8aFCB,SGSHeJ


Try it online in the Pyth Compiler.

Algorithm

The result does not depend on the order of A, so we can assume it to be sorted. This means that B must also be sorted to attain the maximal dot product.

Now, if r1, &hellip; rn are the length of the runs of the sorted A, there are &prod;rk! different rearrangements of the elements of A that still result in ascending order.

Likewise, if s1, &hellip; sn are the length of the runs of the sorted B, there are &prod;sk! different rearrangements of the elements of B that still result in ascending order.

However, this counts all pairings multiple times. If we take the pairs of of the corresponding elements of sorted A and sorted B and define t1, &hellip; tn as the length of the runs of the resulting array, &prod;tk! is the aforementioned multiplier.

Thus, the desired result is (&prod;rk!) &times; (&prod;sk!) &div; (&prod;tk!).

Code

M/*FPJm*F.!MhMrd8aFCB,SGSHeJ

M                             Define g(G,H):
                      SGSH      Sort G and H.
                     ,          For the pair of the results.
                   CB           Bifurcated zip (C).
                                This returns [[SG, SH], zip([SG, SH])].
                 aF             Reduce by appending.
                                This returns [SG, SH, zip([SG, SH])].
      m                         Map; for each d in the resulting array:
              rd8                 Perform run-length encoding on d.
            hM                    Mapped "head". This returns the lengths.
         .!M                      Mapped factorial.
       *F                         Reduce by multiplication.
     J                          Save the result in J.
    P                           Discard the last element.
  *F                            Reduce by multiplication.
 /                  
                          eJ    Divide the product by the last element of J.
                                Return the result of the division.


Verification

I've pseudo-randomly generated 100 test cases of length 6, which I've solved with the above code and this brute-force approach:

Ml.Ms*VGZ.pH

M             Define g(G,H) (or n(G,H) on second use):
         .pH    Compute all permutations of H.
  .M            Filter .pH on the maximal value of the following;
                 for each Z in .pH:
     *VGZ         Compute the vectorized product of G and Z.
    s             Add the products.
                  This computes the dot product of G and Z.
 l              Return the length of the resulting array.


These were the results:

$ cat test.in
6,9,4,6,8,4,5,6,5,0,8,2
0,7,7,6,1,6,1,7,3,3,8,0
3,6,0,0,6,3,8,2,8,3,1,1
2,3,0,4,0,6,3,4,5,8,2,4
9,1,1,2,2,8,8,1,7,4,9,8
8,3,1,1,9,0,2,8,3,4,9,5
2,0,0,7,7,8,9,2,0,6,7,7
0,7,4,2,2,8,6,5,0,5,4,9
2,7,7,5,5,6,8,8,0,5,6,3
1,7,2,7,7,9,9,2,9,2,9,8
7,2,8,9,9,0,7,4,6,2,5,3
0,1,9,2,9,2,9,5,7,4,5,6
8,4,2,8,8,8,9,2,5,4,6,7
5,2,8,1,9,7,4,4,3,3,0,0
9,3,6,2,5,5,2,4,6,8,9,3
4,2,0,6,2,3,5,3,6,3,1,4
4,8,5,2,5,0,5,1,2,5,9,5
6,8,4,4,9,5,9,5,4,2,8,7
8,9,8,1,2,2,9,0,5,6,4,9
4,7,6,8,0,3,7,7,3,9,8,6
7,5,5,6,3,9,3,8,8,4,8,0
3,8,1,8,5,6,6,7,2,8,5,3
0,9,8,0,8,3,0,3,5,9,5,6
4,2,7,7,5,8,4,2,6,4,9,4
3,5,0,8,2,5,8,7,3,4,5,5
7,7,7,0,8,0,9,8,1,4,8,6
3,9,7,7,4,9,2,5,9,7,9,4
4,5,5,5,0,7,3,4,0,1,8,2
7,4,4,2,5,1,7,4,7,1,9,1
0,6,2,5,4,5,1,8,0,8,9,9
3,8,5,3,2,1,1,2,2,2,8,4
6,1,9,1,8,7,5,6,9,2,8,8
6,2,6,6,6,0,2,7,8,6,8,2
0,7,1,4,5,5,3,4,4,0,0,2
6,0,1,5,5,4,8,5,5,2,1,6
2,6,3,0,7,4,3,6,0,5,4,9
1,4,8,0,5,1,3,2,9,2,6,5
2,7,9,9,5,0,1,5,6,8,4,6
4,0,1,3,4,3,6,9,1,2,7,1
6,5,4,7,8,8,6,2,3,4,1,2
0,3,6,3,4,0,1,4,5,5,5,7
5,4,7,0,1,3,3,0,2,1,0,8
8,6,6,1,6,6,2,2,8,3,2,2
7,1,3,9,7,4,6,6,3,1,5,8
4,8,3,3,9,1,3,4,1,3,0,6
1,4,0,7,4,9,8,4,2,1,0,3
0,4,1,6,4,4,4,7,5,1,4,2
0,0,4,4,9,6,7,2,7,7,5,4
9,0,5,5,0,8,8,9,5,9,5,5
5,7,0,4,2,7,6,1,1,1,9,1
3,1,7,5,0,3,1,4,0,9,0,3
4,4,5,7,9,5,0,3,7,4,7,5
7,9,7,3,0,8,4,0,0,3,1,0
2,4,4,3,1,2,5,2,9,0,8,5
4,8,7,3,0,0,9,3,7,3,0,6
8,9,1,0,7,7,6,0,3,1,8,9
8,3,1,7,3,3,6,1,1,7,6,5
6,5,6,3,3,0,0,5,5,0,6,7
2,4,3,9,7,6,7,6,5,6,2,0
4,8,5,1,8,4,4,3,4,5,2,5
7,5,0,4,6,9,5,0,5,7,5,5
4,8,9,5,5,2,3,1,9,7,7,4
1,5,3,0,3,7,3,8,5,5,3,3
7,7,2,6,1,6,6,1,3,5,4,9
9,7,6,0,1,4,0,4,4,1,4,0
3,5,1,4,4,0,7,1,8,9,9,1
1,9,8,7,4,9,5,2,2,1,2,9
8,1,2,2,7,7,6,8,2,3,9,7
3,5,2,1,3,5,2,2,4,7,0,7
9,6,8,8,3,5,2,9,8,7,4,7
8,8,4,5,5,1,5,6,5,1,3,3
2,6,3,5,0,5,0,3,4,4,0,5
2,2,7,6,3,7,1,4,0,3,8,3
4,8,4,2,6,8,5,6,2,5,0,1
7,2,4,3,8,4,4,6,5,3,9,4
4,6,1,0,6,0,2,6,7,4,9,5
6,3,3,4,6,1,0,8,6,1,7,5
8,3,4,2,8,3,0,1,8,9,1,5
9,6,1,9,1,1,8,8,8,9,1,4
3,6,1,6,1,4,5,1,0,1,9,1
6,4,3,9,3,0,5,0,5,3,2,4
5,2,4,6,1,2,6,0,1,8,4,0
3,5,7,6,3,6,4,5,2,8,1,5
6,3,6,8,4,2,7,1,5,3,0,6
9,1,5,9,9,1,1,4,5,7,3,0
1,6,7,3,5,8,6,5,5,2,6,0
2,8,8,6,5,5,2,3,8,1,9,8
0,4,5,3,7,6,2,5,4,3,2,5
5,1,2,3,0,3,4,9,4,9,4,9
5,8,2,2,0,2,4,1,1,7,0,3
0,6,0,0,3,6,3,6,2,2,2,9
2,4,8,1,9,4,0,8,8,0,4,7
3,9,1,0,5,6,8,8,2,5,2,6
5,3,8,9,1,6,5,9,7,7,6,1
8,6,9,6,1,1,6,7,7,3,2,2
7,2,1,9,8,8,5,3,6,3,3,6
9,9,4,8,7,9,8,6,6,0,3,1
8,3,0,9,1,7,4,8,0,1,6,2
8,2,6,2,4,0,2,8,9,6,3,7
1,0,8,5,3,2,3,7,1,7,8,2
$ while read; do
&gt; pyth -c 'M/*FPJm*F.!MhMrd8aFCB,SGSHeJMl.Ms*VGZ.pHAc2Q,gGHnGH' &lt;&lt;&lt; "$REPLY"
&gt; done &lt; test.in
[4, 4]
[4, 4]
[8, 8]
[4, 4]
[8, 8]
[2, 2]
[4, 4]
[4, 4]
[4, 4]
[36, 36]
[2, 2]
[8, 8]
[24, 24]
[8, 8]
[2, 2]
[2, 2]
[6, 6]
[2, 2]
[8, 8]
[2, 2]
[12, 12]
[2, 2]
[8, 8]
[12, 12]
[4, 4]
[12, 12]
[4, 4]
[6, 6]
[8, 8]
[8, 8]
[6, 6]
[4, 4]
[48, 48]
[8, 8]
[4, 4]
[1, 1]
[4, 4]
[4, 4]
[8, 8]
[4, 4]
[12, 12]
[2, 2]
[96, 96]
[2, 2]
[4, 4]
[2, 2]
[6, 6]
[24, 24]
[24, 24]
[48, 48]
[4, 4]
[8, 8]
[12, 12]
[8, 8]
[4, 4]
[2, 2]
[24, 24]
[16, 16]
[2, 2]
[8, 8]
[24, 24]
[4, 4]
[24, 24]
[4, 4]
[12, 12]
[8, 8]
[12, 12]
[4, 4]
[8, 8]
[4, 4]
[16, 16]
[4, 4]
[8, 8]
[8, 8]
[4, 4]
[4, 4]
[4, 4]
[4, 4]
[72, 72]
[24, 24]
[4, 4]
[4, 4]
[4, 4]
[2, 2]
[12, 12]
[4, 4]
[8, 8]
[4, 4]
[36, 36]
[6, 6]
[12, 12]
[8, 8]
[4, 4]
[2, 2]
[8, 8]
[24, 24]
[6, 6]
[1, 1]
[2, 2]
[2, 2]


To verify my submission satisfies the speed requirement, I've ran it with this test case.

$ time pyth -c 'M/*FPJm*F.!MhMrd8aFCB,SGSHeJAc2QgGH' &lt; test-large.in | md5sum
5801bbf8ed0f4e43284f7ec2206fd3ff  -

real    0m0.233s
user    0m0.215s
sys     0m0.019s