Ni!
The algorithms in graph-tool are written in C++, just like the algorithms in igraph are writen in C. In both cases, the C++/C code gets compiled before installation.
Graph-tool's python library, like the higher level libraries for igraph, are only interfaces to the underlying compiled code.
Therefore, there is no relationship between "filtering capabilities" increasing compile time, and the runtime speed or memory consumption of graph-tool.
For the kind of things you describe, if igraph does it within your memory limits, graph-tool should do it as well. And for the numbers you give, it should be orders of magnitude lower than what you're expecting.
Cheers,
.~ยด