Tradeoff between embedded chip and external GPS antennas
A full size patch antenna (normally about 25 × 25 × 4 mm) will typically have a gain of around 5dB and for an SMA connector pair insertion loss for even fairly cheap connectors is likely to be under 0.5dB at 1.5GHz. For coax RG-174 is a pretty popular (and cheap) cable often used on consumer grade GPS antennae. Running the numbers through this Attenuation and power handling calculator over that short distance the loss at GPS frequencies is only 0.3db. So you should still have a net gain of over 4dB.

Most modern receivers will work well with that and for example the Fastrax IT520 documentation recommends a loss of less than 1dB when using a passive antenna which the above combination achieves. In a vehicle application sometimes the effect of too much gain can be mixed, you can for example start picking up weak reflected signals that can cause multipathing effects. Other than extended testing with a particular module there's not really any way to predict that reliably.

For ESD protection I don't really see an issue if you're using an encapsulated antenna and the SMA connectors are normally always mated. But a little extra ESD protection isn't a bad thing and while the low capacitance protection diodes made for that purpose are small they do normally meet all the usual ESD standards.

So in general I'd say give the external passive antenna a shot and compare against an active in some real-world tests. Some of the cheaper antennae are actually quite good, so grab a few of each from a variety of manufacturers and unlike reworking a PCB design they can easily be compared. It sounds like you've talked yourself out of an on-board antenna for other valid reasons, but I don't see signal loss to be significant enough over that short distance to worry about that side of things.