We've installed over 1000 hanger bolts onto a variety of slate, fake slate, yorkshire stone and cotswold slate roofs over the last 2 years, and not had one report of a leaking roof, or cracked slates as a result *.
We've only broken a couple while drilling them, while driving the bolts through them, or while using the bolts to stand on directly, or once the rails are in place, and IIRC those were down to accidentally forgetting to wind the nut high enough up the bolt to avoid it being driven into the slate, so was operator error. There is a definite technique to it, and you need the right kit or you'll destroy every slate you try to drill - we use a high kick/hammer SDS drill from makita, which basically punches through the slate from the inside in the same way that a traditional slaters pick does, rather than actually drilling through it (note, do not try this with anything other than slate).
In light of the reluctance on this forum regarding them, I do intend to revisit a selection of the installations that have been in place the longest to verify that there haven't been any problems since we left, but I really think we'd have known about it with the summer we've just had if there were going to be problems.
We have always taken care not to over tighten the nut compressing the gasket against the slate so that there's still enough flexibility in it to not damage the slate if the bolt flexes in high wind etc, as well as pilot drilling from the inside in the centre of the rafter then redrilling a slightly larger hole in the slate than the bolt on the outside so the bolt isn't forcing the slate apart, and flashing anywhere that there is a danger of water getting under the top slate, or on rougher surfaces etc.
IMO installed with care, hanger bolts are a sounds installation method for most slate roofs, but it really is down to the installation method, which IMO is why the manufacturers won't actually certify the bolts for use on slate themselves.
I should add that a lot of solar thermal manufacturers have been specifying these bolts for this purpose for 20 years+, and are still specifying them precisely because their panels are too heavy for the sorts of tile brackets we tend to use for PV, and result in the brackets cracking the tiles / slates. So they view the hanger bolts as being the options that's least likely to crack the tiles / slates in a situation with greater loading, and the same level of wind and snow loading than PV, so tbh I take the reluctance shown on this forum (and in MCS) towards them with a big pinch of salt.
I may of course live to eat my words if we have to go back and remount every slate system we've installed if the mounting system doesn't prove durable, but I don't see why this should be the case, and can comfortably say that we've had far far less issues with them breaking the slated while standing on them during mounting of the panels than we have with using fully adjustable brackets on rosemary tiles, which I'd take as evidence that it's a more durable solution for slate than that is for rosemaries.
I've also had several very sceptical time served roofers come around to our point of view once they've seen our installation, and even had 1 say they'll happily warranty the roof still on a new build after we've installed using this method.
Please note, this is for info only, don't come crying to me if you use this method and you do get problems down the line, it's up to you as a competent installer to make that judgement call yourself. Personally though we genuinely believe this to actually be the better mounting method, as it disturbs the slate roof the least, and only puts a 10mm diameter hole in it rather than a bracket size hole, which IMO is the best way of minimising damage to the roof and future problems that can stem from that. Time will tell though.
nb - don't even think about trying this on 35mm rafter though, at least not without using noggins for all fixing points.
*does touching a wood effect desk count as touching wood?
