I think if the Yeerk is controlling the morph, it will morph properly. Its probably similar to morphing clothes: if the morpher wants to incorporate clothing into the morph and concentrates on it, it will happen.
Also in book 15, when one of the Animorphs gets a chip implanted in them as a shark, then morphed to fly, the chip didn't shrink. This could be because they didn't realise it was there and didn't incorporate it into the morph.