Chiral spin liquids (CSLs) are time-reversal-symmetry-breaking ground states of frustrated quantum magnets that show no long-range magnetic ordering but instead exhibit topological order and fractional excitations. Their realization in simple and tractable microscopic models has, however, remained an open challenge for almost two decades until it was realized that Kitaev models on lattices with odd-length loops are natural hosts for such states, even in the absence of a time-reversal-symmetry-breaking magnetic field. Here we report on the formation of CSLs in a three-dimensional Kitaev model on a hypernonagon lattice composed of nine-site loops, which differ from their widely studied two-dimensional counterparts; namely, they exhibit a crystalline ordering of the Z(2) gauge fluxes and thereby break some of the underlying lattice symmetries. We study the formation of these unconventional CSLs via extensive quantum Monte Carlo simulations and demonstrate that they are separated from the featureless paramagnet at high temperatures by a single first-order phase transition at which both time-reversal and lattice symmetries are simultaneously broken. Using variational approaches for the ground state, we explore the effect of varying the Kitaev couplings and find at least five distinct CSL phases, all of which possess crystalline ordering of the Z(2) gauge fluxes. For some of these phases, the complementary itinerant Majorana fermions exhibit gapless band structures with topological features such as Weyl nodes or nodal lines in the bulk and Fermi arc or drumhead surface states.