I too have been on PPIs for years (18 to be precise) and have not experienced any side effects as yet.
Surprisingly I wasn't aware that tomatoes cooked or uncooked could cause issues for those with reflux and have never been affected by them, nor for that matter fruits with high citrus contents however tea and coffee that is not decaffeinated plays merry hell with my stomach and oesophagus.
Perhaps with have different tolerances for various fruits and yours is tomatoes.
I don't know what you daily dosage of PPIs is but for the record mine is 2 x 15mg of Zoton FasTab which is the most effective for me rather than the generic omeprazole and lansoprazole that GPs prefer to prescribe due to cost.
I had to jump through hoops to get back onto the FasTab when my GP placed me on the generic alternatives but after "yellow carding" the these meds with the MHRA, he was obliged to return to the status quo and I was back on the FasTab within a couple of weeks.
Perhaps some of the issues you have are with the generic meds you are being prescribed, if indeed you are and perhaps a chat with your GP may be beneficial in resolving some of your issues re tomatoes.