Using Pi-Hole to resolve hostnames to ip addresses should not affect you transfer speed as its only a few small packets being communicated to Pi and back for setting up initial communication.
After that, the resolved remote IP address is cached (with TTL) by the client and the client will not ask Pi again during for example a file download.
You could do a "traceroute" to compare if network route/path changes with or without the Pi resolving, which i think would be highly unlikely but still.
Plus you can most of the times see which box is delaying the most.
For example:
$ traceroute pi-hole.net
traceroute to pi-hole.net (104.24.108.83), 30 hops max, 60 byte packets
1 10.0.0.1 (10.0.0.1) 0.537 ms 0.369 ms 0.374 ms
2 192.168.1.1 (192.168.1.1) 0.759 ms 0.553 ms 0.663 ms
.
.
8 ams-ix.as13335.net (80.249.211.140) 28.528 ms 28.301 ms 28.480 ms
9 104.24.108.83 (104.24.108.83) 28.497 ms 28.599 ms 28.658 ms
EDIT: Sorry am new on forum and this one came up as unread ... didnt notice it was 22days old.