I've extracted frozen and thawed Phalaris by sonication in acidified water on a normal ultrasonic cleaner. The results (by HPLC) agreed closely with extraction by bead beating in a centrifuge tube shaken on a reciprocating saw, and also with larger-scale extractions by various means. I'm working mostly with 5-MeO-DMT, but there's also some DMT present. I don't see any evidence that either alkaloid was degraded by the sonication.
That said, sonication alone doesn't effectively extract from all plant material. For example, it extracts almost nothing from thick, succulent leaves like my Sceletium. I'd expect a professional lab to prefer sonication where possible, but they should confirm that it's working by comparison to other methods, ideally including immediate lyophilization and powdering (or something similarly mechanically aggressive).
Three hours is an unusually long time to sonicate, perhaps suggesting they got bad recovery with shorter times and that their method is thus marginal. If asked, then they should be able to explain why they thought that method was suitable, and if unable then acknowledge the potential issue and perhaps retest. I've unfortunately never worked with any Acacia myself.
I use my ultrasonic cleaner constantly, both to sonicate and simply as a temperature-controlled water bath for evaporation, hot pulls, etc. Beyond extracting from plant material, sonication is effective in dissolving almost anything, especially sticky resins or gums. I wouldn't expect moderately (like 50 C) elevated temperature to hurt these tryptamines, but if low temperature is desired then you can just put ice in the bath.