Yes, part of Beacon's resolution is shuffling it into the deck, so as it resolves it will shuffle into the deck. Where or how you cast it doesn't matter.
Unless they way you cast the spell specifies that you do something else with the spell it behaves normally.
Take the rule for Flashback, for example:
702.33a Flashback appears on some instants and sorceries. It represents two static abilities: one that functions while the card is in a player’s graveyard and another that functions while the card is on the stack. “Flashback [cost]” means “You may cast this card from your graveyard by paying [cost] rather than paying its mana cost” and “If the flashback cost was paid, exile this card instead of putting it anywhere else any time it would leave the stack.” Casting a spell using its flashback ability follows the rules for paying alternative costs in rules 601.2b and 601.2f–h.
So if you use Snapcaster Mage to give Beacon flashback and cast it from your graveyard it would not shuffle in.
Narset's ability has no such instruction. It will shuffle in as part of it's resolution.
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Take the rule for Flashback, for example:
702.33a Flashback appears on some instants and sorceries. It represents two static abilities: one that functions while the card is in a player’s graveyard and another that functions while the card is on the stack. “Flashback [cost]” means “You may cast this card from your graveyard by paying [cost] rather than paying its mana cost” and “If the flashback cost was paid, exile this card instead of putting it anywhere else any time it would leave the stack.” Casting a spell using its flashback ability follows the rules for paying alternative costs in rules 601.2b and 601.2f–h.
So if you use Snapcaster Mage to give Beacon flashback and cast it from your graveyard it would not shuffle in.
Narset's ability has no such instruction. It will shuffle in as part of it's resolution.