I came across this ruling from ayatollah sistani(ha) and although it’s only recommended precaution I still want to clarify it to ensure I’m doing the right thing.

Ruling 990. The recommended precaution is that in prayers one should not stop on a letter that has a vowel, nor join a letter that has a sukūn…

My question:

Does this also apply to thikr of ruku and sujood? for example if I want to recite subhanallah 3 times then if I recite it with the kasra i.e "subhanallahe subhanallahe subhanallah" then I should recite without a pause between each "subhanallah" but if I recite "subhanallah" without the kasra then I should have a short pause between each of the 3 subhanallahs.

Is my understanding correct?

It is not necessarily the same between Quranic recitation and dhikr, but the way you have described is correct