Q:

Does the switch from Ford to Nissan have an in-universe reason?

In the first seasons of Fringe, we see all of the Fringe division drive Fords. The series was sponsored by the Ford Motor Company at the time, as noted in the closing credits.
After

 Peter was removed from the timeline at the start of season 4, 

we see them driving Nissans — or so I noticed in S4E4 "Subject 9". And indeed, there was now a message acknowledging Nissan's sponsorship.
Is there an in-universe reason for that, or did they just switch sponsors?

 The other changes caused by Peter's disappearance are very small and only related to the people he would otherwise have interacted with.

So why are they now driving Nissans instead of Fords? Is there an in-universe explanation?

A:

It's never addressed in-universe; not this issue specifically, and not the breadth of differences between the two timelines in general.
However, Peter's disappearance had a larger impact on the timeline that it at first seems. The most obvious example of this is that a couple of events we saw happen in Season 1 happen again after his return later in Season 4. Those events originally happened almost immediately after Walter and Peter joined the Fringe team in the original timeline. But in the new timeline, it had clearly been years since Olivia busted Walter out of the mental hospital. Events like the creature on the airplane from the first season, or indeed the entire David Robert Jones storyline, had nothing to do with Peter when they started, but nonetheless played out differently in the two timelines.
Given that Walter himself was responsible for so much of the "fringe science" that the Fringe team ends up investigating, it's likely that the lack of Peter in his early life may have resulted in small changes that rippled outward. Any number of reasons -- the most obvious being budgetary and/or administrative changes -- could impact the decision of which vehicles to buy, and since that's would be a wholly insignificant detail to most field agents, it's not surprising that no one brought it up.

