Depends on what "scientific" assumptions are. If you mean, are there some
assumptions that work better for science (or even make it possible when it
might not otherwise be), then, yes, some assumptions are more scientific
than others. Some assumptions are required for science.
If you mean, are there some assumptions that science supports, then, yes,
some are, in a very loose way, SUPPORTED by empirical data, though such data
is not necessary, and such data does not prove positive philosophical
claims. Philosophy can be studied and developed without recourse to any more
empirical data than that available to an average person. The person does not
even need to be able to see.
The deeper question is not about science, of course, but about general
rationality. Are there some philosophical assumptions that are more RATIONAL
than others? Yes.
Assumptions beyond naturalism, for example, require very special evidence.
Naturalism is minimal. The burden of proof is on anyone who wants to assume
or prove anything beyond, or over and above naturalism as a philosophical
claim, and as a methodological premise for science.