My tires say tubeless, but they have inner tubes. What's up with that?
There are several answers for this one. One has to do with the style of the rims. For whatever reason, probably cost, the tubeless type of wire spoke rims as used on the R/GS series were not used on the F's. Because the spoke nipples are inside the bead of the tire much care and considerable luck would be needed to keep air inside the tires, one reason for the tube. Others have to do with riding off road. With the low pressures used for off road riding, it would be very easy for a tubeless tire to pop it's bead off the rim, and having a tube inside gives a little extra insurance against punctures. The plus side of this is that should a puncture ever happen, a simple fix of the tube gets you back on your way. Many off roaders carry "Slime" or some other puncture repair along with some way to re-inflate the tire, either CO2 cartridges or a pump. If a flat happens, you're back on your way relatively quickly. With a tubeless tire, while emergency plugs are available, they are just that and a puncture pretty much dictates a new tire for safety reasons.
It is fine to put tubes in tubeless tires. In fact all tubeless motorcycle tires say, either on the tire or in the manufacturer's literature words to the effect, "Install tube when used on tube-type rim."