Can two strings be matched as disjoint subsequences of a string?
Case k=2

Perhaps you can use the following polynomial time dynamic approach:

Keep a table $T_i$ of $(|S_1|+1)(|S_2|+1)$ pairs, in which element $(x,y)=1$ if and only if after scanning $i$ elements of the reference string $S$, $x$ characters of $S_1$ have been found, and $y$ characters of $S_2$ have been found (without overlaps).

Every pair of the table $T_0 (i=0)$ is zero except for the pair $(0,0)=1$.
Copy $T_i$ to $T_{i+1}$ and read the next character $c=S[i+1]$  from $S$; if in $T_i$ there is an entry $(x,y)=1$ such that $S[x+1]=c$ then in $T_{i+1}$ set $(x+1,y)=1$; if in $T_i$ there is an entry $(x',y')=1$ such that $S[y'+1]=c$ then in $T_{i+1}$ set $(x',y'+1)=1$.

At the end of the scan, $S$ contains the merged distinct copies of $S_1$ and $S_2$ if and only if $(|S_1|,|S_2|)=1$.

Simple example:

S  =  a b a a c
S1 =  a a c
S2 =  b a  

S    0,0  0,1  0,2 1,0 1,1 1,2 2,0 2,1 2,2 3,0 3,1 3,2
     1    0    0   0   0   0   0   0   0   0   0   0  &lt; T0
a    1    0    0   1   0   0   0   0   0   0   0   0  &lt; T1
b    1    1    0   1   1   0   0   0   0   0   0   0  &lt; T2
a    1    1    1   1   1   1   1   1   0   0   0   0  &lt; T3   
a    1    1    1   1   1   1   1   1   1   0   0   0  &lt; T4       
c    1    1    1   1   1   1   1   1   1   1   1  [1] &lt; T5


Case k fixed

The same approach above can be used for any fixed $k &gt;2$ (the table size grows polynomially).

Case k not fixed

If $k$ strings are given as input, and $k$ is NOT FIXED: in that case there is a quick reduction from the 3-PARTITION problem which is strongly NP-complete, so it remains NPC even when the input numbers are represented in unary.

Given a set of $A = \{x_1,x_2,...,x_{3m}\}$ of $3m$ positive integers (that can be specified in unary), and a target sum $B$ we must find $m$ disjoint subsets $A_1,A_2,...,A_m \subseteq A$ of $3$ elements ($|A_i|=3$), and the sum of the elements of each subset must be $B$.

Over alphabet $\{a,b,c\}$, set:


"reference" string $S = a^3 \; b^B\; c^3 \; a^3 \; b^B\; c^3 \; ... a^3 \; b^B\; c^3 \;$ ($a^3 b^B c^3$ repeated $m$ times)
for $i = 1,...,3m$ set string $S_i = a \; b^{x_i} \; c$


Informally: the $a^3$ parts of $S$ force to match $3$ of the $S_i$s (otherwise some $S_i$ will not be included); the $c^3$ parts force to "close" $3$ of the $S_i$s. And the  $b^B$ blocks (there are $m$ of them) must be filled exactly with the $b^{x_i}$ substrings of $3$ distinct $S_i$.

Small example:

3-PARTITION instance: $A = \{ 3,  2, 1, 5, 4, 3\}, B=9, (m=2)$

S  = aaa bbbbbbbbb ccc aaa bbbbbbbbb ccc
S1 = a bbb c
S2 = a bb c
S3 = a b c
S4 = a bbbbb c
S5 = a bbbb c
S6 = a bbb c