Yes, these warnings are a concern. Be aware that the travel advice dispensed by, say, the UK Foreign & Commonwealth Office (and their international equivalents) usually errs on the side of caution (read the travel advice for your own country of origin to confirm this!) but for Malaysia Sabah is immediately highlighted as an area of concern, especially the resorts of Semporna, Sipada and Mabul. I think you are right to pause and ask for more details before booking anything here if there is evidence Westerners are being targeted; too many don't even bother to research the security of a region. Having said that, take things in perspective. There have "only" been three or four kidnapping incidents in ten years and consider how many tourists go there every year. Everything is a "risk", even getting on a plane - you just have to work out how real the risk is and then work out whether it's worth taking - and if you do take it, how to minimise it.
I went to Sabah 6 years ago but that was just to Kota Kinabalu, towards the west. I felt very safe there and didn't bat an eyelid, but the eastern resorts might be a bit different. I also travelled in Laos when there were armed robberies on the Highway 51 (there had been one the previous year) and went to some places in the south of Thailand when there was terrorist activity. I was extra-vigilant but nothing untoward happened.
Above all else you don't want this to be on your mind when you're on holiday - you're going there to relax, not worry! - so only you will know if you can perceive and rationalise the size of the risk and put it behind you for the duration of your stay.
More details here:
Malaysia travel advice