When a card modifies how many copies of that card a deck can have, does that affect the sideboard?
Rule 100.4 clearly distinguishes between the deck and the sideboard, by using the word "also". That is, a player must have a deck of minimum size and may choose to have a sideboard of maximum size.
Rule 100.4a again makes this distinction, and clarifies that the deck and sideboard together may contain a maximum of four copies of the same card. This ensures a person cannot "accidentally" end up with more than four copies of the same card when making changes between deck and sideboard, or "accidentally" mix up the two sets of cards to disguise excess use of one card.
Rule 100.4c gives further insight into the separation between decks and sideboards, by telling us that all cards not in the decks of either player are in the sideboard. A card cannot both be in the sideboard and in the deck, therefore the sideboard cannot be part of the deck.
Consider the outcome of counting the sideboard as part of the deck: someone could pick just 45 (or 25!) cards for actual use in the match, shuffled to form their library. If this was intended, the rule writers could, and given the clarity of the Rules as a whole, assuredly would, have said so.
All told, this would mean a card that says "You may only have one copy of [Card Name] in your deck" would not disallow having three copies in the sideboard as well. However, none of those other copies could be brought into the game by an effect that accesses the sideboard (if such an effect were to be written). To avoid the loophole, the card should say "... in your combined deck and sideboard".