What buildings have six-way vaulted crossings. Cathedrals commonly
have four-way vaulted crossings, typically surmounted by a cupola. I
want to find structures where six barrel (or similar) vaults intersect
in a common point. High security prisons often are built with a
starlike floor plan, but they have conventional ceilings and roofs.
Please supply examples only with vaulted (e.g. barrel, romanesque,
gothic) ceilings.

Searched for hexagonal dome+ read through some promising articles
Try:
Italian Baroque
Sant Ivo della Sapienza- dome
Francesco Borromini
Rome, Italy
1642-1650

Cappella della Santa Sindone aka Chapel of the Holy Shroud- dome
Guarino Guarini 
Turin, Italy
1667-1694

There was less information for these two:
Concepción Coepopan Chapel, Mexico
Shirvanshah Palace

I would also suggest looking east- especially at mosques (Sinan is a
good architect to look at) as well as Indian architecture. Would you
be interested in structures with muqarnas? There are many six and
twelve division examples in various mosques.