Yes, Wireshark can be used alongside Connection Emulator. That said, we have not specifically tested running both on the same machine, so there are some nuances to be aware of. In particular, when Connection Emulator is configured to drop packets, it is difficult to predict whether Wireshark will capture a packet before or after our driver processes it — so the capture may not accurately reflect what the remote end actually receives.
If this turns out to be an issue in practice, Connection Emulator has a built-in alternative: it can write two PCAP log files per session — one capturing packets before processing and one after. This effectively gives you a complete record of every session without needing Wireshark running on the same machine.