Large language models (LLMs) are increasingly deployed in agentic systems, where a fundamental task is mapping user intents to relevant external tools. Errors in tool selection can have severe outcomes, such as unauthorized data access, even without modifying the agent's underlying model. Existing evaluations measure performance on curated, benign benchmarks. However, a pipeline's behavior in deployment depends on the tool pool the agent actually encounters, which in open registries is shaped by third parties. We introduce LLMCert-T, the first statistical framework that returns \textbf{high-confidence upper bounds on the probability that a tool-selection pipeline satisfies a declared safety specification under a realistic tool distribution}. LLMCert-T models tool-selection evaluation as a Bernoulli estimation problem, drawing inserted-tool sequences from a distribution that the safety specification fixes. To evaluate robustness against realistic deployment conditions, we instantiate this distribution as a stochastic process that generates inserted-tool sequences round by round, conditioning each round on the agent's selection in the previous round. LLMCert-T aggregates the per-trial outcomes into a one-sided Clopper-Pearson upper bound on the probability that the specification is satisfied. By returning this bound as a certificate with statistical guarantees over the inserted-tool sequence distribution, LLMCert-T makes safety claims intuitive, actionable, and comparable across models, retrievers, mitigations, and registry policies. Across popular BFCL and OpenAPI tool pools, LLMCert-T shows that current LLM agents remain fragile under Distractor Selection and Top-N Saturation specifications: their certified correctness upper bounds drop to approximately 20\%, far below their clean-pool lower bounds.