I've bought 6 instruments from Japan, and sold one of them back to someone living there when I no longer needed it, but all these transactions were prior to international shipping getting a lot more complicated.
I did 4 shop sales, all buying second hand from Ishibashi. All went smoothly and I even got a discount on one bass which had sticker residue on the body that hadn't been noticeable in the original sale photos but was picked up by Ishibashi when they did their quality check before shipping. Shipping costs were very good, I wasn't able to match the price when shipping in the opposite direction as a private seller, and VAT and Import Duties were close to my guesstimates so no nasty surprises there.
I also brought back a new guitar on each of the two occasions that I visited Japan. The instruments I bought were all ones that were almost impossible to find for sale outside of Japan - Atlansia Solitaire Bass, Fernades Pie-zo Bass Gothic Hello Kitty Edition, Tokai Talbo Bass, Tokai Talbo Jr Guitar, Yamaha BJ-5B (a limited edition of 50 models) and a Yamaha EZ-EG. I certainly wouldn't use it just to try and save a few pounds on something that could be imported for you by a UK distributor.
Some Japanese shops are simply not set up to deal with foreign sales and even now in the 21st Century you'll get no reply when they realise that you are not in Japan. However if it's an eBay sale that is visible to potential buyers outside of Japan, then the seller should be set up to deal with enquiries in other languages - in this respect we have a massive advantage being English speakers - and international shipping.
As has been said there's a whole extra level of protection if you buy through eBay, so check the seller feedback and bid away.
Edit to say Japan is VERY service focused, and if anything does go wrong you can guarantee that it happen here in the UK where it is completely out of the control of the Japanese seller.