It's a well-known issue unfortunately. I call it the overloading problem (although I'm not part of the developing team).

What bothers me is that it seems to have worsened with version 1.3.3. It's just a vague feeling I have, but I can't quite shake it.

I think I'll try to work out a comparison by playing ver 1.3.2 and 1.3.3 successively and timing my progression to see if the lag starts earlier in the latter version.

Don't forget that, with a bit of luck, you can find another S-Nav in the Archive Room.

It's randomized. I also noticed an S-Nav in SCP-106's containment area today, on the shelves near the control panel.