Yes, it can go both ways. The only problematic warning of the three warnings you refer to is the second.
The first is just a warning during the solution of the steady state, but there is still a check whether the solution actually is a steady state. So nothing can go wrong here.
Similarly, the third one refers to the initialization of the Kalman filter. Any problems here should be minimal as initial conditions usually die out quickly.
The warning about an inaccurate solution is more tricky. In theory, the results may be inaccurate and the effect on the likelihood might go both ways. Unfortunately, there is no way to know the size of the error as there is no other way to compute the actual correct solution. The accuracy of the likelihood depends on the accuracy of the solution and is of the same order (see also http://onlinelibrary.wiley.com/doi/10.1111/j.1468-0262.2006.00650.x/abstract and http://onlinelibrary.wiley.com/doi/10.3982/ECTA7669/abstract). So unless you think there is a massive problem with your solution for some parameters you should be fine.