Generating functions and computer algebra systems to the rescue! In the product
$$ \prod_{i=1}^6 \sum_{k=0}^6 z^k q^{ki} = (1+zq+z^2q^2+\cdots+z^6q^6)\cdots (1+zq^6+z^2q^{12}+\cdots+z^6q^{36}),$$
the term $z^3q^{12}$ in $(1+zq^4 + z^2q^8 + z^3q^{12} + z^4q^{16} + z^5q^{20} + z^6q^{24})$, for instance, corresponds to $i = 4$ occurring $n_i = 3$ times. That is, in each term, the exponent of $z$ gives the frequency (your $n_i$) and the exponent of $q$ gives the contribution to the sum (your $in_i$ in (2)).
In the expanded product, since exponents sum, the terms with $z^6$ correspond to length 6 sequences and terms with $q^{21}$ have the desired sum. So the coefficient of $z^6q^{21}$ gives the number of your sequences. (One notation for this is $[z^6q^{21}]\prod_{i=1}^6 \sum_{k=0}^6 z^k q^{ki}$.) Using your favorite computer algebra system (Mathematica for me), this is easily found to be 32, corroborating VTand's count.
To better understand the connection, the sequence $(1,1,4,5,5,5)$ in VTand's list corresponds to the term
$$z^2q^{2\cdot 1} \cdot z^0q^{0\cdot 2} \cdot z^0q^{0\cdot 3} \cdot z^1q^{1\cdot 4} \cdot z^3q^{3\cdot 5} \cdot z^0q^{0\cdot 6} = z^2q^2 \cdot zq^4 \cdot z^3q^{15} = z^6q^{21}$$
for two 1s, no 2s, no 3s, one 4, three 5s, and no 6s. The sequence $(1,4,4,4,4,4)$ corresponds to
$$z^1q^{1\cdot 1} \cdot z^0q^{0\cdot 2} \cdot z^0q^{0\cdot 3} \cdot z^5q^{5\cdot 4} \cdot z^0q^{0\cdot 5} \cdot z^0q^{0\cdot 6} = zq \cdot z^5q^{20} = z^6q^{21}$$
for one 1, no 2s, no 3s, five 4s, no 5s, and no 6s. Etc. The 32 sequences listed in the comment correspond to $32z^6q^{21}$ in the expansion.
In case you're interested in other sums besides 21 still with 6-sided dice with possible values $\{1,2,3,4,5,6\}$ on each face, here are some relevant terms from the expansion:
$$\cdots + 29z^6q^{18} + 30z^6q^{19} + 32z^6q^{20} +
32z^6q^{21} + 32z^6q^{22} + 30z^6q^{23} + 29z^6q^{24} + \cdots$$