Suppose I'm Visser Three's paranoid Lieutenant that got the job after the last three (no, lets say twelve) sub-vissers were hacked to pieces, eaten in a rage, or just transferred to accidentally wounded Taxxon bodies. Was Tom worth the security risk? You can't just run out a portable Yeerk pool every time a Controller's family goes on a vacation. All Yeerks, especially as one as *ahem* ambitious as Tom's need to be controlled by the higher-ups.
We can just as easily surmise that -I mean Tom's Yeerk so wily deceived Visser Three and stole the Escafil Device and Blade ship right under his nose months after this happened- Tom'sY had already been marked as difficult to control or excessively ambitious. That's how the Empire seemed to run. Maximum paranoid, minimal pragmatism.