Your intuition is correct. Here is a more precise mathematical description. I find that this chapter (of the book Monte Carlo theory, methods and examples by Art B. Owen) is a useful reference for material on Latin Hypercube sampling.
Assume that the LHS samples are taken on the unit interval $[0,1)$ as described in Section 10.3 of the book chapter. Let $X$ denote the vector of samples from the 1000 sample LHS. Let $Y$ denote the vector of samples from the ten combined 100 sample LHS. How are $Y$ and $X$ different?
Even in one dimension, the different 'levels' of stratification imply that (the distributions of) these samples differ. Choose a particular dimension - then consider the number of samples falling into the subinterval $[0,0.001)$ within the chosen dimension. The basic properties of LHS (10.6 and 10.7 in the book chapter) imply that, for $X$, the number of samples in this subinterval is fixed at one. However, for $Y$, the number of samples in this subinterval will be $\text{Binomial}(10,0.1)$, which is clearly random, not fixed.
In multiple dimensions, other differences between $X$ and $Y$ will be apparent. Choose two dimensions and consider only the samples residing in a small square such as $[0,0.01)\times[0,0.01)$ within the chosen two dimensions. For $Y$ the location of a sample inside this square places no constraints on the locations of other samples inside this square. However, for $X$ the location of a sample inside this square restricts the locations of other samples inside the square ('unthreatened rooks').
See also this question which approaches the same situation from a slightly different angle (asking whether the estimates obtained from this kind of modified LHS are still unbiased).