If only there was a globally unique set of short two-letter names for every country that could be used as prefixes to enforce uniqueness while still allowing every country to manage their own internal waypoint list.
I'm sure they thought about this at some point. Airports already have a country-code prefix. (For example, airports in the Continental US always start with K.)
For whatever reason, by convention navaids never use a country prefix. Even when it would make sense - the code for San Francisco International Airport is "KSFO", but the identifier for the colocated VOR-DME is just "SFO". (Sometimes this does make a big difference, when navaids are located off site - KCCR vs CCR for Concord Airport vs the off-site Concord VOR-DME, for example.)
It's even worse for NDB navaids, which are often just two letters.
Either way, we're stuck with it because it's baked into aircraft avionics and would be incredibly expensive to change at this point.
If only.