Nothing in the manual other than the fact that the holes are there for lifting.
Yes, round stock bars all the way thru. This is a common thing on all sorts of machinery, and particularly so on things that don't have full sheet metal enclosures. A lot of fully enclosed machines have holes thru the base castings too, although they may not be readily accessible once the machine is fully assembled. They are there for ease of movement of the machine thru the plant during manufacture. Once you get into machines large enough that forklift handling isn't practical, there's often removable access panels on the enclosures for access to the holes or other features originally used for movement thru manufacturing.
To lift with a crane you'd just use bars long enough to extend past the table and then slip the eye of a choker or nylon sling over each bar end. Probably would want to use a spreader bar if you need to keep the hook height to a minimum due to overhead clearance issues.
Alternately, if round stock isn't available, you could run chokers or slings across underneath the base, block them apart with wood, pad them where they cross edges, and lift the machine with no problem.
Another option is to remove one hook and run an alloy lifting chain thru each hole. The downside to this is the angle of the chains is going to put significant upward force on the table, so you'd need to pay attention to that and whether there's a possibility of damaging the table. That's something I really haven't looked at on our punch since I've never needed to lift it like that.
Personally, I'd lean toward slinging under the base as opposed to running chains thru the holes purely because of the forces on the table. In either case, I'd definitely use a spreader bar unless I had room to use a set of 4 hook slings 12 ft or so long above the machine.
FWIW, way more than half of the things lifted every day with cranes do not have specific provisions for lifting built in. 99% of the time this is a non-issue for competent riggers and people in the lifting business.
Because of the general configuration of that particular turret punch, if I had to rig it with slings under the base I'd also add a chain or short choker, depending on the required length, from the hook to the head area of the machine just to make sure it didn't flip backward. There's a lot of weight concentrated toward the rear with the way its built.
Honestly, that machine won't pose any great problem for lifting to anyone experienced in the trade.