I definitely seem to recall being able to jump higher/farther in vanilla Half-Life 1 and Half-Life: Source, but perhaps I am not remembering correctly. But yes, in the old versions of ‘Black Mesa’ you had to manually crouch while jumping to raise your legs.
During my playthrough I at first found it a funny feature bringing you back to the olden times of Half-Life, but after my left hand started hurting after a good bunch of levels (played through them like mad, and loved it!) I really preferred not having to crouch while jumping.
So (shameless plug) I messed around with a few keybind aliases and came up with the following:
https://forums.blackmesasource.com/showthread.php?t=13723
It’s a small tweak set adding some extra (and optional) controls to the bottom of the keyboard options menu that allow you to toggle duck and perform automatic duck jumps, and a few other keybinds (some of them considered cheats).
Try them out if you like and drop a few replies with ideas for improvement. The keybinds are gathered in a separate ‘Sjakal’ category at the bottom of the keyboard options menu, and you can mix and match them with the original keybinds if you prefer manual duck jumping or sprinting and so on.