I doubt it. There are occasionally reports that changes in things like name or level affect routing and there may be some minor effects. But in general the level should not affect the route.
On the other hand, there have been a large number of reports, many recent, of waze routing straight/U rather than a simple left. I think the issue is that waze knows that there is an average delay to make the left onto the ramp, but as no one passes the ramp to make the u-turn, waze is not accurately guessing how fast the u-turn is.
Waze seems to able to
route correctly. So it seems to me to be more likely to be an issue with the speed data than an issue with the levels. However, the levels don't really do much anymore, so I would go ahead and change them and see what happens.