It's probably best to start with what the timing model/s show. The most common model is the slow corner, which is what Altera says will be the worst case delay for each path. This accounts for many factors, with the main ones being PVT, Process, Voltage and Temperature. So if you got the slowest die out of the fab(which passes qualification), had it at the slowest(highest) temperature and the slowest(lowest) voltage allowed by the device specs, then it would be equal to or faster than this number. So consider these numbers to be a ceiling.
There is also a slow corner analysis. This can be used in static timing analysis to analyze the "fastest" a delay can be. Is what you'll find is that there is a wide range of values the delay can be. For example, if you have a pure delay of 12ns in your simulation(which uses the slow corner), and the fast corner showed the delay at 6ns, then the delay could be anywhere between that and the design needs to be able to account for that. (It's impossible to create silicon that doesn't vary. All FPGA/ASIC designs deal with this...)
Now, if you have two signals coming out at 12ns difference in the simulation, they probably won't have as much variance because you're not looking at raw delays, but at the difference in the delays. This means the PVT differences will track each other. This falls more into the realm of on-chip variation(OCV) analysis.
If I lost you, that's all right for now. Static timing analysis can be extremely complex, but most designs can get away without having to grasp the complexities.
Now my very first suggestion is to not gate the clock. This is one of the strongest recommendations I can make. Understandably there are situations where this must be done, but in your case you have a PLL which can be used to make a full speed and half speed clock. The edges will be very closely aligned(enough that you shouldn't have to worry about hold time violations), and the PLL will also reduce PVT variations in the clock tree(this is what a PLL does. It removes clock tree delays, variations, and does clock synthesis).
Synchronous design is by far the easy to do timing analysis and when it can be done, is highly recommended. Most of that talk about timing models can be ignored. (It's still relevant at the IOs, but that's a whole other thread.) I probably haven't answered everything, but hopefully that's a glimpse of the affects at play here.