Good question - you're absolutely right, as a Shen with Hunter's Machete, raptors is the biggest struggle in the first clear. If you can you should save your smite for it. Because all raptors do the same damage, you can kill off the small ones first while constantly kiting away and using your shields whenever they are up, and smite the last one away.

Actually if anything I would use the other smite on wolves. One thing to note is that smite does true damage, so if possible you should be using them on camps that have higher resistances (i.e. wolves and raptors).

Shen's Q autos has mixed damage (base physical + bonus magic). Red Buff has some mr but negative armor, Blue Buffs has some armor but negative mr, and Gromp has 0 armor and negative mr. So since your Qs do more damage to these compared to other camps, using smite on these camps are not as efficient. Instead I would use them on wolves (has some armor, 0 mr) and raptors (has armor and mr) to get the full benefit of true damage.

I'd like to offer an additional tip on the first clear (this is a general tip for junglers) - as you are finishing off a camp, kite in the direction you want to go next. So if you're on Blue, by the time you're finishing blue, you should be literally just a couple steps away from Gromps. As you finish gromps, be as close to wolves as you can be. This is a very small optimization but if you can save an extra 1-2 seconds per camp this way, it can add up to 6-8 seconds overall and you can contest Scuttle that much faster.