There's a big 'yes, but...' here.
Yes, most major cities have >1 major rail hub.
That's not usually been the result of rational transit planning though. Most rail networks in those cities were built by private operators. In some cases terminals were the result of government bans on railways downtown; London's scattering of terminals outside of its (historic) CBD is the result of government legislation banning railways through the City, which in turn required the construction of the first underground lines to connect the terminals.
Thankfully most American cities were more rational in their approach and built joint ("Union Stations"). So, outside of NYC n Chicago, I don't think any other American city has more than one major rail hub.
In any case, almost all European and Asian cities which ended up stuck with multiple terminals have been in the process of trying to unify their system through quite large (and expensive!) tunnel projects. Looking at most regional or commuter rail systems in Europe, it's a bit redundant to talk of 'major stations' since very few commuter rail services terminate anywhere downtown.
So it's a bit senseless to set about trying to make a second hub downtown for commuter rail. In future intercity or HSR services could be shunted off to a different station somewhere downtown without too much impact, but what would the upside be?