Small crack along windowsill

Unfortunately, the windows probably should have been addressed before the new siding went on. Doing the windows before putting on new siding would have given you the option of using new construction vinyl double hung with J-channel build into the frames. It also would make repairing or replacing rotted framing members much easier.

However, since you already have the new siding up (would like to see a pic of the window with the new siding in place) you may have to use replacement type windows. If you have rotted frames, those will have to be replaced and the new replacement windows sized to the opening AFTER the frame is fixed. Of course you can carefully calculate the opening based on what you intend to use to reframe the opening, but that can be risky for an amateur. Keep in mind, replacement windows usually have to be ordered to you exact size and are not returnable if you measure them wrong. Always a good move to have supplier measure and order the windows for you. After you install the new replacement windows, you may have to install some new extension jams and exterior trim in order to fit snugly to the new siding. Don't forget to use Ice & Water shield under the finish frame/ over rough opening framing and caulk all areas where water could possibly get in.

I generally use a clear-coat Varnish finish on my outdoor painting projects to reduce wear damage and to extend the life of the paint. You can get this as a spray or a paint. This is the easiest and cheapest solution but provides only moderate protection.

For superior protection:

You could attach a piece of plexiglass or tempered glass with adhesive or standoff mountings. I'm not sure if the adhesive would be visible between the glass and the voids in the surface. Using an attractive glass with standoff mountings would provide a very clean and modern look. A quick google search for glass standoffs shows that you can get them as short as .5in/1.25cm.

A final thought would be to make a mold around the windowsill and pour in an acrylic resin. This would fill in the voids in the surface and provide a very sturdy glass-like finish.

Here is a link to pouring acrylic on a table. You can adapt the instructions for your windowsill.

Note that using an adhesive or acrylic resin is more a less a PERMANENT installation. It will be very hard to remove either. The varnish or glass+standoffs is considerably easier to remove later if you want to repaint or change the look.