You could also look at Blue Star Ferries, who do the long distance Greek domestic services but can be used for short hops too. Although both Dodekanisos Seaways and Blue Star serve Nissyros and Kalymnos, there are alternatives.
South from Kos there are the Panagia Spiliani and various local excursion boats operating to Nissyros, both from Kos Town and Kardamena ports.
North from Kos there is a frequent local service by both fast ferries and vehicle carriers from Mastichari (Kos) to Kalymnos.
Kalymnos has its own regional ferry, the Nissos Kalymnos, which heads both north to Samos via half the Dodecanese and west to Astypalea, depending on the day of the week.
www.gtp.gr is the best place to look for Greek domestic ferries as it is a travel trade website rather than a booking system, so shows just about everything. Not so good on Turkey-Greece sailings though as it doesn't include some of the Turkish operators.
There are at a minimum morning and afternoon sailings between Bodrum and Kos every day with several shipping companies on the route, and Turgutreis-Kos has sailings several days a week.
The changes on the international services are partly due to government action. Increased enforcement of existing Customs regulations made cross-border shopping day trips less attractive, from both sides of the border. Changes in Turkish immigration procedures have made it harder for some nationalities to get access other than for day trips without obtaining visas in advance, and the once regular flow of expats living in Turkey leaving the country every few months to get an exit stamp in their passports so resetting the clock on their stay in the country has stopped because they can now easily get residence permits. All in all, just fewer passengers, but the port fees have gone up on both sides.