Are you sure all those packets are actually leaving the iPhone?
Maybe Apple imposes bandwidth restrictions on apps, as I told you on stackoverflow you should really ask this question in the Apple Bluetooth mailing list, where there are several helpful Apple engineers that could potentially help you.
Otherwise you really need to specify what chipsets you are using if you want to get something out of these questions.
EDIT: ok, you are using the CSR chipset, then I suggest contacting CSR directly and posting your question here:
https://lists.apple.com/mailman/listinfo/bluetooth-dev
EDIT2: a sniffer could certainly help you see whether those packets are actually being sent by the iphone and not being received by the CSR chipset, or else it is just that the iPhone is never actually sending them over the air
I take it that the question is whether or not the radio frequency (RF) signals between the two devices will be blocked by the components in a car, when one of the devices is outside and one is inside.
Metal and other conducting materials are efficient at blocking RF. Also placing an antenna close to metal is also likely to "de-tune" the antenna, meaning it will not be as efficient on the intended frequency. Also 2.4GHz signals are not great at penetrating and have shorter range than lower frequencies. Say 900MHz would work almost 3 times as far with the same TX and RX properties. Cars can also come with metallic paints which block RF and the wind screen's coating commonly also blocks RF.
That being said, a typical bluetooth low energy device with a TX power of 0dBm and an RX sensitivity of say -90dBm gives you a theoretical 90dBm "link budget". To carry a 2.4GHz RF signal in free space for 3m, you need a link budget of 50dBm plus at least 10dBm of so called "fade margin". (Simple calculator: http://www.qsl.net/pa2ohh/jsffield.htm) Now this leaves us with a margin of 30dBm for attenuation caused by the car chassis.
RF will radiate in all directions and bounce off of materials. The question becomes, is there a way for the RF to travel between the two devices which would cause less than 30dBm of fading/attenuation. This very well may not be a straight line, but may instead be for example by bouncing off the road or getting wave-guided through the ventilation :).
Causing 30dBm attenuation is actually not very easy as the RF tends to "leak" through any and all routes. You'd be hard pressed to find locations in a car where there isn't some route that the RF finds that causes less than 30dBm of attenuation. There are some numbers for common building materials http://www.moonblink.com/store/attenuation_at_24ghz_.cfm that give you an idea of typical losses for materials.
In summary: Yes it is possible for two devices to communicate when one is placed outside of the car and one is placed inside of the car. Just don't place the antenna straight onto metal which would detune it and block a lot of RF paths.
Best Answer
If you data will fit into an advertising packet payload, then that is the lowest power possible way to get that data delivered to a receiver (or receivers). To send an atomic data set via advertising, you only need to send a single packet. A connection at very least would require a send followed by a receive.
You also indicate that you could go hours between data packets. With advertising, you can send your packets spontaneously as you like- as long as the receiver gets the packet when you do send it then the transfer is good.
Advertising packets are also much simpler to create. You could save processor cycles by laying out all the static parts of the packet in memory one and then very quickly updating only the dynamic data fields before a send.