We study nonparametric covariance function estimation for functional data observed with noise at discrete locations on a $d$-dimensional domain. Estimating the covariance function from discretely observed data is a challenging nonparametric problem, particularly in multidimensional settings, since the covariance function is defined on a product domain and thus suffers from the curse of dimensionality. This motivates the use of adaptive estimators, such as deep learning estimators. However, existing theoretical results are largely limited to estimators with explicit analytic representations, and the properties of general learning-based estimators remain poorly understood. We establish an oracle inequality for a broad class of learning-based estimators that applies to both sparse and dense observation regimes in a unified manner, and derive convergence rates for deep learning estimators over several classes of covariance functions. The resulting rates suggest that structural adaptation can mitigate the curse of dimensionality, similarly to classical nonparametric regression. We further compare the convergence rates of learning-based estimators with several existing procedures. For a one-dimensional smoothness class, deep learning estimators are suboptimal, whereas local linear smoothing estimators achieve a faster rate. For a structured function class, however, deep learning estimators attain the minimax rate up to polylogarithmic factors, whereas local linear smoothing estimators are suboptimal. These results reveal a distinctive adaptivity-variance trade-off in covariance function estimation.