It's not implementation-dependent in the sense that this is a
mathematical operation performed on your matrix. However, it is very
much matrix-dependent.
If your matrix is diagonalizable and $A=XDX^{-1}$, then zeroing out
some element adds a small perturbation matrix $E$, so the new
eigenvalues will be (assuming the matrix $X$ does not change much)
$$ X^{-1}(A+E)X = D + X^{-1}EX. $$
The difference in $D$ has norm bounded by
$$ \|E\| \kappa(X), $$
where $\|E\|$ depends on the magnitude of the elements you drop, and
$\kappa(X)$ is the condition number of the matrix of eigenvectors.
If your matrix $A$ is
normal (i.e.,
$AA^t=A^tA$), then $X$ is unitary and $\kappa(X)=1$, so this is fine.
If your matrix is not normal, you need the concept of its
pseudospectrum, defined as the set
$$ \Lambda_\epsilon(A) = \{z \mid z \text{ is an eigenvalue of $A+E$
with $\|E\| \leq \epsilon$} \}. $$
An equivalent definition, which is easier to compute with, is
$$ \Lambda_\epsilon(A) = \{z \mid \|(zI-A)^{-1}\|\geq \epsilon^{-1} \}. $$
There is a good survey of pseudospectra and their properties in
Pseudospectra of Matrices by Trefethen (it includes a nice gallery of matrices whose pseudospectra are much larger than their spectra: one might think that the pseudospectrum should be a collection of small $\epsilon$-sized disks around the eigenvalues, but that is really not right at all). In general, you cannot just
assume that the pseudospectrum is well-behaved and that the
perturbations are negligible. You can, however, compute $\kappa(X)$ and estimate the resulting error; you can also compute the pseudospectrum directly.
In some sense, dropping small matrix elements is fine: either they don't matter, and the new results are just as accurate as the original, or they do matter, and your original results are just as inaccurate as the new results.