Question 1: In the statement of Theorem 3.1, $T_{l_k}$ is a $k$-simplex in the set $E$; the conclusion $|T_{l_k}| > 0$ is precisely the conclusion that this simplex is not the trivial (empty) one.
Question 2: At the beginning of section 3 (page 4), the authors define simplices in terms of a certain ``distance'' $\| \cdot \|$. One simplex $T$ is an isometric copy of another, $T'$, if $T'$ can be obtained from $T$ by a transformation $O$ that preserves distances between points within the simplex, i.e. for $x_i, x_j$ points of $T$ we have $\| O(x_i) - O(x_i) \| = \| x_i - x_j \|$. You can see in Lemma 3.2 that such a transformation can always be taken to be an orthogonal transformation of $\mathbb{F}_q^d$.