Your question conflates "recognizing the existence of a territory/organization/state" and "recognizing the geographical boundaries of a territory/organization/state."
Your example is "a Crimean based website using a .ru domain." I don't see any difference between "a Crimean based website using a .ru domain" and, say, "a U.S.-based website using an .io domain" (like, e.g., my blog hosted on github.io). I live in the U.S. and maintain a website in the .io domain; that doesn't even remotely suggest that the U.S. is physically part of the British Indian Ocean Territory.
You also seem to be worried about some sort of magic-words trap where someone could say "Aha, you visited www.unitedstates.io, therefore you are legally bound to recognize that the United States is part of the Indian Ocean Territory!"
Likewise, if certain people located physically in Crimea happen to run websites under .ru, that doesn't mean that Crimea is physically part of Russia; and if you happen to visit www.crimea.ru, that doesn't imply any kind of legal agreement that Crimea is (or is not) part of Russia.
Getting back to the conflation... There is definitely more of an argument to be made that the existence of the .ru TLD implies that someone, somewhere, recognizes the existence of Russia. However, as Jörg W Mittag pointed out in the comments, domain-name TLDs are more or less based on the two-letter abbreviations maintained by the U.N.'s Statistics Division, and the U.N.'s Statistics Division very clearly states:
The designations employed and the presentation of material at this site do not imply the expression of any opinion whatsoever on the part of the Secretariat of the United Nations concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries.
This doesn't directly address your concerns about phone-number country codes, but I can't imagine any reason for the logic and rationales re: phone numbers to "work" any differently from the logic and rationales expressed above re: TLDs.
UPDATE: @MichaelZ, from your comments below, I surmise that you don't really get how DNS works. When you direct your browser to (let's say) www.crimea.ru, all that happens is that your computer looks up that name in a big distributed "phone book," starting at the top ("at the root") and then descending: you ask the root "What's the IP address of www.crimea.ru?" and the root says "I don't know, but on the subject of .ru domains, I trust a.dns.ripn.net, whose IP address is 220.127.116.11." So then your computer asks 18.104.22.168 "What's the IP address of www.crimea.ru?" and 22.214.171.124 says "I don't know, but on the subject of .crimea.ru domains, I trust ns1.ht-systems.ru, whose IP address is 126.96.36.199." So then your computer asks 188.8.131.52 "What's the IP address of www.crimea.ru?" and 184.108.40.206 says "Oh, that's 220.127.116.11." So then your computer sends an HTTP GET request (or whatever you're interested in doing) to 18.104.22.168. If it's HTTP or HTTPS, it'll also send some header data that basically says "Hello 22.214.171.124! A little bird told me you were www.crimea.ru; is that right?"
There's a lower level, "IP" (Internet Protocol), that handles the routing of packets to these various IP addresses. In a sense, the Internet Protocol "recognizes" the relationship between certain IP blocks and certain geographical regions of the Earth. However, it does not recognize political boundaries; there's no concept of an IP address saying "I am Russian" in the same way that a domain name could say "I am Russian (.ru)." (And, again, a domain name can "say" it's Russian only in the same sense that it can "say" it's the Indian Ocean; that doesn't necessarily have any bearing on geographical reality.)
Anyway, does this help clarify why none of this technology stuff has any bearing on geographical or political boundaries?