Navmesh addons may only work after you close the game entirely, so give it a try.
Close the game and open it again.

This was mentioned by: @Lagota https://gtm.steamproxy.vip/id/Laqota
Thank you.

If you are not sure, check out the collection below and verify if you are subscribed to everything.

https://gtm.steamproxy.vip/sharedfiles/filedetails/?id=3574816937

If there are addons conflicting with the navmesh or the map, or even with "Bon the Rabbit", you should check those out first and disable them.

There seem to be at least two "Bon the Rabbit" addons that people are using so I will distinguish them here.

My testing was done with this one ->
https://gtm.steamproxy.vip/sharedfiles/filedetails/?id=3541699236

The alternative one is this one -> https://gtm.steamproxy.vip/sharedfiles/filedetails/?id=3541514355

Is it still not working? Follow along the list below, and if a step does not solve the problem, follow onto the next one.


THIS LIST IS A WORK IN PROGRESS
=====================================================================

STEP ONE - Basics first and a clean run.
- Assuming you have subscribed the collection above, please disable everything that's not in it and go into the game, this way you are certain that there are no conflicting addons.


STEP TWO - Tweaking the rabbit's settings.
- If "Bon the Rabbit" is still not going into the vents, check his settings.

Navigate to Spawn Menu -> Utilities -> Bon the Rabbit -> Bon Settings
Here you should tweak the "Detection Settings"; try increasing them individually or together.


STEP THREE - Tweaking "DrG Base" settings.
- Try to tweak the setting of the nextbot's base, not his own settings.

Navigate to Spawn Menu -> DrGBase -> Nextbot settings -> AI Settings
First, attempt to increase the target distance in the "Detection" section.

Consider increasing it all the way to the maximum value allowed by it and see if the rabbit goes into the vents.

As a last resort, toggle omniscience ON, which will make "Bon the Rabbit" immediately start chasing you with the added bonus of never stopping until he catches you.


STEP FOUR - Checking out the navmesh.
- Open up your console and type the following commands: sv_cheats 1 -> nav_edit 1

This will allow you see the navmesh itself, so now you should look into the vents or spaces where you have to crouch in order to cross to another room.

If there is no navmesh there, it can be one of two things.

Option one is you did not restart the game and so the mesh did not load in properly, this can happen and that is ok.

Option two, but less likely, is that I forgot to mesh the vent, in which case you should notify me immediately so I can update the addon to make it better for everyone else.

- To stop viewing the navmesh, simply open up the console again and type nav_edit 0


STEP FIVE - Longer Leaps.
I was able to reach this possible solution thanks to
@Crazy -> https://gtm.steamproxy.vip/id/1580937558166/

Thank you so much for taking your time to try and solve this with me.

-This step will take a little longer, but follow these steps carefully.

• Number one: Uninstall the map by unsubscribing.
  
• Number two: Close the game, quit it entirely.
  
• Number three: Open the game, close it again without doing anything else.
  
• Last Step: Install the map by subscribing and open the game afterwards.

Go into the game and check if the "Bon the Rabbit" goes into the vents and crawls accordingly.



STEP SIX - Different Approach
This possible solution was mentioned by:
@Medajoltz -> https://gtm.steamproxy.vip/profiles/76561198211064289

Thank you for helping me and this community out in order to further enjoy these addons!

-In this step you will need to go into the game files, so be patient and follow these instructions carefully.

• Number one: Go into the game -> Addons.
  Here you should find this addon and press uninstall, closing the game afterwards.
  
  
• Number two: Go to your steam library -> Right click Garry's Mod -> Select Properties.
  A menu should pop up.
  
  
• Number three: Click the third tab from the top named "Installed FIles" -> Select Browse....
  This will open your file explorer in a folder named "GarrysMod".
  
  
• Number four: In this folder, follow the following path: garrysmod -> maps
  Here you will see all the map-related files.
  
  
  !Be very attentive with the steps below; we will be deleting files!
• Number five: delete a file named: gm_k9.nav
  
  
• Number six: While still inside the "maps" folder, go into a folder named "graphs".
  Here you should delete the following files:
  -> gm_k9.ain
  -> gm_k9.ain.ztmp
  
  Disclaimer: There could be more files inside related to the map inside these folders given there are future updates or anything of that sort, but I urge you to keep file deletion exclusively to files which follow these two rules:
  
  1 - They are either inside the "maps" folder or the "graphs" folder - 1
  
  2 - They have "gm_k9" in their name - 2
  
  I do not take responsibility if you decide to delete files that don't follow both rules.
  
  
• Number Seven: Open Garry's Mod, and in your addons, re-enable the navmesh addon.
  
  
• Number Eight: Close the game and open it again,

After all of these steps were followed, go into the map and check if everything works now.

To accomplish this, open your console and type the following commands in succession:
-> sv_cheats 1
-> nav_edit 1

Look into the vents and crawlspaces.

Remember, if you need to stop viewing the navmesh, simply type: nav_edit 0.