- Do emulated switches perform worst than actual switches?
Yes, of course software performs worse than hardware. Physical switches do their switching in hardware, and are able the get wirespeed switching, but software switches are much slower.
- Are emulated switches are good method to measure the throughput
performance of a network?
No, not even close.
- Is GNS3 a good choice to do such measurements or any alternatives?
No it is not a good choice for network measurements (possible to compare different GNS3 topologies, but not against the real world). Unfortunately, product or resource recommendations are explicitly off-topic, except on Software Recommendations and Hardware Recommendations. You will not find any software switches that compare with physical hardware switches in speed.