Yes, the old deities are really coming back. Along with the list of old deities in the Forgotten Realms section of the gods listed in the updated basic rules, (and the gods listed amongst many pantheons in the Player's Handbook) there is also the "Sundering" story line. The Player's Handbook lists 39 deities for the Forgotten Realms setting with their domains and symbols. And 24 "non-human deities" which are shared between Greyhawk and Forgotten Realms.
During the Sundering the worlds of Toril and Abeir (which were united during the Era of Upheaval) are being separated from each other. During this time, the various gods are creating "chosen" mortals who are intended to bring power to the gods, in the hope that when "things are settled" these gods will have the power required to remain a god. There seems to be confusion amongst the gods as to what Ao actually has in mind as he re-writes things.
Noted events during the Sundering are the diminishing of Spellplague effects, magic changing its nature to the way it worked in the past, such that old spellbooks work and recent ones do not. "The Weave" has new prominence, and most importantly for this question, various gods are found to either not be dead, to be re-united, or to be recreated through various events. It seems that in the various divine schemes to "get enough followers" all divine who have a "chosen", get chosen to remain a god, in a fun twist of the meaning of the "chosen".
According to Netheril: Empire of Magic (N:EoM), at the time of the Netherese there were very few human deities and each one of them carried very many portfolios. It seems like as the millennia went by, those portfolios got shared by many new powers.
For Mystryl, the list went like this: Magic, spells, the weave, wizards, spellcasters, energy, creativity, knowledge, invention, song, time, spring (page 49 of The Winds of Netheril).
We can compare this list with the portfolios given in the FR Adventures (FRA) and Faiths & Avatars (F&A) sourcebooks. We see that every portfolio except Time is covered: Azuth (mages, energy according to FRA; wizards, spellcasters according to F&A), Oghma (knowledge according to FRA; knowledge, invention according to F&A), Lathander (spring according to FRA; spring, creativity according to F&A), Milil (song), and of course Mystra (magic, spells, the weave).
Given that every other one is somehow covered, and the great many commonalities between N:EoM and F&A, I would agree with Carcer's statement and say Time appears to have been intentionally left out by TSR. (F&A lists Julia Martin with Eric Boyd as designers. For N:EoM, Julia Martin is listed under "additional design" and Eric Boyd is listed as a proofreader.)
There is one final curiosity: Amaunator is mentioned (in both N:EoM and F&A) to have misinterpreted some godly contract and wanted to preside over passage of time, but decided not to interfere with Mystryl. It looks like after Mystryl's demise, he still did not claim Time. So perhaps Mystra could still be the "hidden inheritor" of the portfolio and might someday claim it openly. It might also be worth mentioning that three "time gates" that allow characters to travel back to the Netherese period were still active as of 1370DR, and they were being protected by Mystryl's magic (N:EoM). It would be an interesting scenario to have Midnight/Mystra sending an avatar/proxy to meet her old self, Mystryl.
On a related note: Here is a list of powers from F&A who grant major access to the sphere of Time to her/his speciality priests: Amaunator, Auril, Chauntea, Cyric, Eldath, Kelemvor, Leira, Mask, Mielikki, Myrkul, Mystra, Shar, Silvanus, Sune. We broadly see that they are mostly deities of nature, death, or deception. If you really want to assign the portfolio of Time in your own game, consider one of these.
Deities followed by chronomancers
There is an article with the title Chronomancy & the Multiverse, version 1.1 by Roger E. Moore, published as "an updated and expanded excerpt from the Chronomancer", a 2e accessory. The article was made public by the WotC on their free downloads for previous editions site. This article has a section of the effects of chronomancy in the Realms, and relates time with deities of knowledge and writing. It is stated:
Native chronomancers are usually devout followers of both a deity of magic (e.g., Mystra) and a deity of time or history (e.g., Deneir or Oghma), serving as historians and information collectors. Elven chronomancers of Labelas Enoreth are possible. Shou Lung, in Kara-Tur, might have a secret, officially approved group of chronomancers, probably Historians, working for the Emperor.
Best Answer
No, but the Dead Three are still around
Several gods died during the Time of Troubles, notably including the Dead Three: Bane, god of tyranny, Bhaal, god of murder, and Myrkul, god of death. However, gods are difficult to destroy in the Forgotten Realms, and all three of the dead gods have devised schemes to return to power. Bane’s plot was successful, and he has supplanted the Godson who inherited his portfolio. Bhaal’s scheme was the main plot of the Baldur’s Gate video games. Myrkul appeared in the Neverwinter Nights video games, but so far he still appears to be a dead god, rather than a god of death.
Therefore, the entries for Bhaal and Myrkul currently appear to be there primarily for historical interest, for DMs who want to use them in the past of the Realms, or who want to feature their schemes to return to power. They do not indicate that Kelemvor has lost or changed his portfolio – yet.