A many-particle system must posses long-range interactions in order to be hyperuniform at thermal equilibrium. Hydrodynamic arguments and numerical simulations show, nevertheless, that a three-dimensional elastic-line array with short-ranged repulsive interactions, such as vortex matter in a type-II superconductor, forms at equilibrium a class-II hyperuniform two-dimensional point pattern for any constant-$z$ cross section. In this case, density fluctuations vanish isotropically as $sim q^{alpha}$ at small wave-vectors $q$, with $alpha=1$. This prediction includes the solid and liquid vortex phases in the ideal clean case, and the liquid in presence of weak uncorrelated disorder. We also show that the three-dimensional Bragg glass phase is marginally hyperuniform, while the Bose glass and the liquid phase with correlated disorder are expected to be non-hyperuniform at equilibrium. Furthermore, we compare these predictions with experimental results on the large-wavelength vortex density fluctuations of magnetically decorated vortex structures nucleated in pristine, electron-irradiated and heavy-ion irradiated superconducting BiSCCO samples in the mixed state. For most cases we find hyperuniform two-dimensional point patterns at the superconductor surface with an effective exponent $alpha_{text{eff}} approx 1$. We interpret these results in terms of a large-scale memory of the high-temperature line-liquid phase retained in the glassy dynamics when field-cooling the vortex structures into the solid phase. We also discuss the crossovers expected from the dispersivity of the elastic constants at intermediate length-scales, and the lack of hyperuniformity in the $x,-y$ plane for lengths $q^{-1}$ larger than the sample thickness due to finite-size effects in the $z$-direction.
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