The probelm with the smith machine is that it does a few things for you that are definitely not optimal.
1. It stabilizes the bar for you, taking most of the core out of the equation. Which means when you do transfer over to real barbell squats, you'll have to significantly drop the load back down to build back into it, and by that point, you might have learned a wrong way to setup which means you'll be starting back from square one anyway.
2. It keeps you in a fixed bar path - doesn,t account for your body type/dimensions, and as such is going to be hard on your joints down the line. And even if it's one of those free standing smith machines (my gym has one where the bar will move on an horizontal plane as well as vertical), it's still on rails and will not give you the same feedback as a real squat.

If you have access to a squat rack, you definitely should go for that right away. The motor pattern is different and whatever progress you make on the smith machine will only partially translate to your squatting strength in the end.

If you are trying to build a solid base, but are still feeling squeamish about the barbell squat, the goblet squat is a better option than the smith machine, because it definitely engages your core muscles a LOT (probably even more than the barbell squat) while requiring a similar (albeit a little more upright) stance and technique. You won't be able to use quite as much weight, so you might need to go in a rep range above 5 for a bit. But it will definitely prepare you better for what's ahead IMO.

I hope that helps

And as for whether you should count the bar or not on the smith machine - I think that sucker has an approximal weight of like 20lbs tops considering the leverages and the rail. But I used it like, once , for squats in my entire life, so I could be wrong! xD

i'll also come back to add: the rule that i trust is 'always, always do your first set with the bar'. it's not even about weight for the first sets; it's just about taking a reading on how your body's doing, whether anything's tight, whether something feels 'off' etc etc.

mark rippetoe's advice in his book starting strength is:

1. start with the bar. and i quote/paraphrase: 'always, always start with the bar, every workout'.
2. after one or two sets add 5 or 10 pounds, if you're happy with form. do a few sets.
3. if that's going well and you're still feeling strong, add 5 or 10 more.
4. repeat step 3 until you reach the weight where you feel like you can't add anymore without starting to lose your good form.
5. do three sets at that weight.
6. call it a workout.
7. eat a cheeseburger (this one is mine).

rippetoe's program is 3 sets at working weight, but you can adapt to the sl version of 5.