Multi-pitch estimation (MPE) typically predicts which pitches are active in a mixture, but not which instrument or source produced them. This paper investigates a lightweight slot-attention framework for multi-instrument MPE (MI-MPE), where a mixture CQT is mapped to an unordered set of source-like pitch maps. The model uses permutation-invariant Hungarian matching to avoid fixed output semantics and treats the number of slots as an upper bound on the number of active sources. We further study two modular extensions: a self-supervised timbre encoder that provides training-time targets for slot-level timbre embeddings, and a polyphony branch that regularizes the pitch density of mixture- and slot-level predictions. Experiments show that Hungarian matching substantially improves instrument family decomposition on URMP. Stem-level prediction remains more challenging: timbre and polyphony supervision improve selected configurations, but do not consistently resolve source assignment. The results suggest that slot-based architectures are a promising direction for source-aware MPE, while highlighting the need to couple auxiliary musical cues to slot identity more carefully.