The only reasons I could think of why they're that long is they were replaced and they got the measurements wrong or used what was available in a pinch to get underway again, or perhaps there were line cutters installed at one time though I don't think for your size shafts the cutter assemblies would have been so thick that they're required that much of a gap. Another possibility would be that the geometry inside the boat changed for some reason; a repower, stringer job, engines were moved for some reason, etc.
A good prop shop should have no problem resizing those or are you replacing the existing ones for another reason? If you're resizing the existing ones, have them checked to ensure they're straight first. If they aren't, cut new ones instead of straightening and cutting the old ones. Straightening can sometimes result in them bouncing back to their bent position over time. While they're off, send your props in to get checked too, that shouldn't cost you anything unless they report needing some tuning. While you're under there, check to ensure your struts are straight and not bent. If they're bent, take them to the prop shop too. Check to ensure the strut bearings are in good shape, if they aren't, now's the time to replace them.
Before you pull the shafts out, check their alignment through the struts and stern tubes through the hull to ensure the shafts are centered through each of them. This will give you an idea if you're in for additional work after you get the shafts back. If they aren't centered, you'll need to do engine alignments and or strut alignments. That final work though should only be done with what you know are straight shafts, and final engine alignments should be done after she's back in the water for a day or so but you can check and get things close while she's on land. In the end, you have a max of .003" to work with all around between the tranny flange and shaft coupler.
If you don't currently have them but were thinking about dripless shaft logs, now's the time to pull the trigger if they're in the budget.
Can you tell I'm trying to get you to BOAT (Break Out Another (Ten) Thousand)
