Yes all the DLP onsite hotels have baggage store rooms. I have stayed at both Santa Fe and Sequoia Lodge and have used the baggage store at both hotels.
I think official check in time at the onsite hotels is 2 pm. Many people arrive as early as they can on check-in in day to maximise their time in the park. If you arrive say at 7 am on your check in day, you go to hotel reception as normal. You will be given your park ticket and breakfast time coupons and the hotel will note on their system that you have arrived. You then take your bags to the storage area, get a ticket (its free) and then head into the parks. Depending on how early you arrive, you could make it for EMH
In the afternoon, depending on your party size and who is with you, you could all go back to the hotel to get your room, or just one person can go back. When you go back, you just go to reception, show your documents again and you will get your room keys. You then can take your bags from the storage area.
Make sure to ask when you leave your bags at the storage area what time they close at, so that you don't leave it too late to come back.
On check out day, its the same. You can check out as early as you like, and depending on the luggage store opening hours leave your bags. I did this on my last day so that I could go to EMH and spend as long in the park as possible on my last day.
Staying at an onsite hotel, even for one night is well worth it for the following reasons
EMH - Extra Magic Hours
This is where the park opens for 2 hours in the morning just for onsite guests. When you check in to an onsite hotel you get a hotel easypass which is scanned at the turnstile with your regular park ticket. Main Street USA , Fantasy Land and Discovery Land are usually open and there are about 6 rides attractions open. Uusually they have Buzz and Peterpan open, which are high wait times during the day, both can get up to nearly 2 hours wait in the daytime but during EMH they are either walk on or have 5 to 10 minute waits.
EMH is a great time for photos. Its about the only time you can get a photo of the castle with no one in the background.
Character Meets during EMH
They used to have character meets during breakfast at the onsite hotels but last year it was switched to in the park during EMH as too many locals and non hotel guests were turning up. Now the hotel guests get an exclusive meet and greet time in the park during EMH
Breakfast in the Park during EMH
Disney do this to ease congestion in the hotels during breakfast time so it is not always available. When you are checking in and getting your breakfast time coupons, ask if breakfast in the park is available during your stay. If it is you will be given a coupon for one of the restaurants in the park, usually Plaza Gardens during EMH. It is a great way to start the day, as you have already been in the park and on the rides and now having something to eat, while the rush of general public are wizzing past on Main Street trying to get to the Lands
Rope Drop
Even if you don't want to be in the park for the full 2 hours of EMH, it is worth heading into the park for the last 30 minutes, ie 30 minutes before general admission time. This way you can take your time and head directly to the rides / Lands which are not open and be at the top of the queue. The CM's drop the rope to open the lands at the general admission time and you are then the first into the lands and onto the rides, while the main rush of general public are still halfway down Main Street.
Shopping Service
When you stay at an onsite hotel you can use the shopping service. This means that when you shop before 3 pm you tell the CM when you are paying which hotel you are staying at. You get a form to fill in, one part is attached to your shopping and you keep one part. You are then told when and where the pick up point is at your hotel. This means you don't have to carry your shopping bags around all day.
Hope you have a great day and come back and give us your thoughts 
