Did viking longboats in fact have shields on the side of the ships?

Yes, archaeological evidence strongly suggest that at least some warships did but, considering the vast numbers of ships that were built during the Viking age - and in many different locations - we cannot assume that all Viking Longboats had shields along the side as only a small percentage have been recovered. Further, it's hard to know in what situations the shields were placed along the side of the ship.

On the archeological evidence,

An interesting feature of the war vessel is the uppermost board or plank, which carries the so-called "Shield List", where all the shields of the warriers [sic] were tied up. They were painted in various colours, usually made of tough wood, mainly oak. To that group of vessels belong the so-called "King" or "Chieftan" vessels of luxury class, wider and more roomy than the normal vessels.

Source: Per Bruun, 'The Viking Ship'. In 'Journal of Coastal Research, Vol. 13, No. 4 (Autumn, 1997)'

One example is the Gokstad ship, a decorative war vessel.

The Gokstad vessel...is 23.2 m long and 5.25 m wide in the middle. The depth from railing to keel was 1.95 m. It has 16 boards or planks on either side. Board No. 3 from above had 16 oar-holes on either side. To these holes 32 shields were fastened with consecutive overlapping. Shields were painted alternatively yellow and black. Thirty-two oars were found and the remains of three rowboats, the largest about 10 m long. The number of shields indicates a crew of about 70 men, making two shifts for rowing. The chieftan was buried around the year 900 AD.

Source: Bruun

The Gokstad was built around 890 and was "a fast and flexible ship that was suitable for voyages on the high seas." When the ship was excavated in 1880,

The remnants of thirty-two overlapping shields, alternately painted yellow and black, were fixed to each side....Securely tied, they hung from a batten on the uppermost or sheer strake (and not slotted behind a rail on the outside of the ship, as with Skuldelev 5).

There is also the Oseberg ship, another Norwegian vessel.

The Oseberg vessel, similar to the Gokstad vessel is 21.4 m long, beam width 5.1 m and depth railing to keel is 1.58 m. It has 12 board planks on either side,... The upper board plank has 15 oarholes on either side. The shield plank is rather thin.

Source: Bruun

Per Bruun cites another example of a ship with shields, known as a Skuldelev 5, probably built in Ireland. This is at the Vikingeskibsmuseet (Viking Ship Museum), in Roskilde in Denmark, near where many ships were found. Below, a museum reproduction shows how the shields were held.

"A wooden 'list' used as a shield rack (a narrow strip of wood cut from the edge of a board, with spacers to provide a narrow gap between the list and the ship, shown here) running along the outside of the gunwale behind which the crew could place their shields, shows that the vessel Skuldelev 5 was undoubtedly a warship. It is an example of the smallest category of warship, a snekkja, as mentioned in written sources from late Viking times and the early Middle Ages." Text and image source: Viking Ships of Roskilde

The National Museum of Denmark concurs that the evidence from Skuldelev 5 indicates shields along the side:

The Skuldelev 5 warship from Roskilde Fjord has given us valuable knowledge about how shields were mounted on the side of a ship. Along one side of the ship the remains of a so-called shield rack are preserved.

and attributes their function as a defensive one "against incoming spears and arrows." The article then goes to note that

Test sailings with a similar shield rack have, however, demonstrated that a ship’s sailing capacity is reduced considerably when shields are mounted along its side. It is therefore probable that the shields were not mounted until immediately before military action.

Artwork also provides some evidence. Unfortunately, the details as to how (and when) the shields were attached to the ship (if at all) tend to be unclear (not surprising given these are mostly stone engravings). Possibly the best depiction is on an 8th or 9th century picture stone in Gotland, Sweden.

"Picture Stone from Smiss in Stenkyrka". Source: viking.archeurope.info

Viking age stone, Gotland. Source.

"Picture Stone from Broa in Halla....The ship depicted on the stone does not rank among the larger vessels, but is well equipped with shields along the gunwale and a resolute crew.". Dated circa. 700–800. Source: viking.archeurope.info

There are other stone engravings, such as this Elaljurate Carving on a Sledge Shaft which show the shields a little more clearly, but then there are also stone engravings which show ships without shields along the side. The logical conclusion to draw from this is that the presence of shields along the side of a ship depended on a variety of factors.

Finally, there is also some evidence from coins but, again, it is unclear how the shields were attached.

Coin, c. 800 – 825, found at Ribe, Denmark. Source: Amazing Treasure of Viking Coins Discovered at Ribe