The distinctions among Lamport clock (scalar logical clock, in your term), vector clock, and matrix clock lie in that they represent different levels of knowledge.
For vector clock $vt_i[1 \ldots n]$ in site $i$, the entry $vt_i[k]$ represents the knowledge the site $S_i$ has about site $S_k$. The knowledge has the form of "$i$ knows $k$ that $\ldots$".
For matrix clock $mt_i[1 \ldots n, 1 \ldots n]$ in site $S_i$, the entry $mt_i[k,l]$ represents the knowledge the site $S_i$ has about the knowledge by $S_k$ about site $S_l$. The knowledge here the form of "$i$ knows $k$ knows $l$ that $\ldots$".
Intuitively, we can do more things with more knowledge.
The following description is mainly quoted from [1]:
Vector clocks and matrix clocks are widely used in asynchronous distributed message-passing systems.
Some example areas using vector clocks are checkpointing, causal memory, maintaining consistency of replicated files, global snapshot, global time approximation, termination detection, bounded multiwriter construction of shared variables, mutual exclusion and debugging (predicate detection).
Some example areas that use matrix clocks are designing fault-tolerant protocols and distributed database protocols, including protocols to discard obsolete information in distributed databases, and protocols to solve the replicated log and replicated dictionary problems.
For matrix clock, we notice that
$min_k(mt_i[k,i]) \ge t$ means that site $S_i$ knows that every other site $k$ knows its progress till its local time $t$.
It is this property that allows a site to no longer send an information with a local time $\le t$ or to discard obsolete information.
[1] Concurrent Knowledge and Logical Clock Abstractions Ajay D. Kshemkalyani 2000